ImmersedBoundaryMorseInteractionForce< DIM > Class Template Reference

#include <ImmersedBoundaryMorseInteractionForce.hpp>

Inheritance diagram for ImmersedBoundaryMorseInteractionForce< DIM >:

Collaboration diagram for ImmersedBoundaryMorseInteractionForce< DIM >:

Public Member Functions
	ImmersedBoundaryMorseInteractionForce ()
virtual	~ImmersedBoundaryMorseInteractionForce ()
void	AddImmersedBoundaryForceContribution (std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &rNodePairs, ImmersedBoundaryCellPopulation< DIM > &rCellPopulation)
void	OutputImmersedBoundaryForceParameters (out_stream &rParamsFile)
double	GetWellDepth () const
void	SetWellDepth (double wellDepth)
double	GetRestLength () const
void	SetRestLength (double restLength)
double	GetLaminaWellDepthMult () const
void	SetLaminaWellDepthMult (double laminaWellDepthMult)
double	GetLaminaRestLengthMult () const
void	SetLaminaRestLengthMult (double laminaRestLengthMult)
double	GetWellWidth () const
void	SetWellWidth (double wellWidth)
Public Member Functions inherited from AbstractImmersedBoundaryForce< DIM >
	AbstractImmersedBoundaryForce ()
virtual	~AbstractImmersedBoundaryForce ()
bool	GetAdditiveNormalNoise () const
void	SetAdditiveNormalNoise (bool additiveNormalNoise)
double	GetNormalNoiseMean () const
void	SetNormalNoiseMean (double normalNoiseMean)
double	GetNormalNoiseStdDev () const
void	SetNormalNoiseStdDev (double normalNoiseStdDev)
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	mWellDepth
double	mRestLength
double	mLaminaWellDepthMult
double	mLaminaRestLengthMult
double	mWellWidth

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractImmersedBoundaryForce< DIM >
void	AddNormalNoiseToNodes (ImmersedBoundaryCellPopulation< DIM > &rCellPopulation)
Protected Attributes inherited from AbstractImmersedBoundaryForce< DIM >
bool	mAdditiveNormalNoise
double	mNormalNoiseMean
double	mNormalNoiseStdDev

Detailed Description

template<unsigned DIM>
class ImmersedBoundaryMorseInteractionForce< DIM >

A force class for use in immersed boundary simulations. This force implements Morse-potential-like links between nodes in adjacent immersed boundaries (https://en.wikipedia.org/wiki/Morse_potential). The well width is a constant interaction strength, the rest length is an equilibrium bond distance, and the well width is a parameter governing the profile of the curve.

Definition at line 57 of file ImmersedBoundaryMorseInteractionForce.hpp.

Constructor & Destructor Documentation

ImmersedBoundaryMorseInteractionForce()

template<unsigned DIM>

ImmersedBoundaryMorseInteractionForce< DIM >::ImmersedBoundaryMorseInteractionForce

(

)

Constructor.

Definition at line 40 of file ImmersedBoundaryMorseInteractionForce.cpp.

~ImmersedBoundaryMorseInteractionForce()

template<unsigned DIM>

ImmersedBoundaryMorseInteractionForce< DIM >::~ImmersedBoundaryMorseInteractionForce ( )

virtual

Destructor.

Definition at line 51 of file ImmersedBoundaryMorseInteractionForce.cpp.

Member Function Documentation

AddImmersedBoundaryForceContribution()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution ( std::vector< std::pair< Node< DIM > *, Node< DIM > * > > &  rNodePairs, ImmersedBoundaryCellPopulation< DIM > &  rCellPopulation  )

virtual

Overridden AddImmersedBoundaryForceContribution() method.

Calculates the force on each node in the immersed boundary cell population as a result of cell-cell interactions.

Parameters

rNodePairs	reference to a vector set of node pairs between which to contribute the force
rCellPopulation	reference to the cell population

Implements AbstractImmersedBoundaryForce< DIM >.

Definition at line 56 of file ImmersedBoundaryMorseInteractionForce.cpp.

References Node< SPACE_DIM >::AddAppliedForceContribution(), Node< SPACE_DIM >::ContainingElementsBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetAverageNodeSpacingOfElement(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetAverageNodeSpacingOfLamina(), ImmersedBoundaryCellPopulation< DIM >::GetInteractionDistance(), ImmersedBoundaryCellPopulation< DIM >::GetIntrinsicSpacing(), Node< SPACE_DIM >::GetRegion(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::NodesInDifferentElementOrLamina(), Node< SPACE_DIM >::rGetLocation(), and ImmersedBoundaryCellPopulation< DIM >::rGetMesh().

GetLaminaRestLengthMult()

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::GetLaminaRestLengthMult

(

)

const

Returns

mLaminaRestLengthMult

Definition at line 184 of file ImmersedBoundaryMorseInteractionForce.cpp.

GetLaminaWellDepthMult()

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::GetLaminaWellDepthMult

(

)

const

Returns

mLaminaWellDepthMult

Definition at line 171 of file ImmersedBoundaryMorseInteractionForce.cpp.

GetRestLength()

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::GetRestLength

(

)

const

Returns

mRestLength

Definition at line 159 of file ImmersedBoundaryMorseInteractionForce.cpp.

GetWellDepth()

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::GetWellDepth

(

)

const

Returns

mWellDepth

Definition at line 147 of file ImmersedBoundaryMorseInteractionForce.cpp.

GetWellWidth()

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::GetWellWidth

(

)

const

Returns

mWellWidth

Definition at line 197 of file ImmersedBoundaryMorseInteractionForce.cpp.

OutputImmersedBoundaryForceParameters()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::OutputImmersedBoundaryForceParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputImmersedBoundaryForceParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Implements AbstractImmersedBoundaryForce< DIM >.

Definition at line 133 of file ImmersedBoundaryMorseInteractionForce.cpp.

References AbstractImmersedBoundaryForce< DIM >::OutputImmersedBoundaryForceParameters().

serialize()

template<unsigned DIM>

template<class Archive >

void ImmersedBoundaryMorseInteractionForce< 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 ImmersedBoundaryMorseInteractionForce.hpp.

References ImmersedBoundaryMorseInteractionForce< DIM >::mLaminaRestLengthMult, ImmersedBoundaryMorseInteractionForce< DIM >::mLaminaWellDepthMult, ImmersedBoundaryMorseInteractionForce< DIM >::mRestLength, ImmersedBoundaryMorseInteractionForce< DIM >::mWellDepth, and ImmersedBoundaryMorseInteractionForce< DIM >::mWellWidth.

SetLaminaRestLengthMult()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::SetLaminaRestLengthMult

(

double

laminaRestLengthMult

)

Set mLaminaRestLengthMult.

Parameters

laminaRestLengthMult

the new value of mLaminaRestLengthMult

Definition at line 190 of file ImmersedBoundaryMorseInteractionForce.cpp.

SetLaminaWellDepthMult()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::SetLaminaWellDepthMult

(

double

laminaWellDepthMult

)

Set mLaminaWellDepthMult.

Parameters

laminaWellDepthMult

the new value of mLaminaWellDepthMult

Definition at line 177 of file ImmersedBoundaryMorseInteractionForce.cpp.

SetRestLength()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::SetRestLength

(

double

restLength

)

Set mRestLength.

Parameters

restLength

the new value of mRestLength

Definition at line 165 of file ImmersedBoundaryMorseInteractionForce.cpp.

SetWellDepth()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::SetWellDepth

(

double

wellDepth

)

Set mWellDepth.

Parameters

wellDepth

the new value of mWellDepth

Definition at line 153 of file ImmersedBoundaryMorseInteractionForce.cpp.

SetWellWidth()

template<unsigned DIM>

void ImmersedBoundaryMorseInteractionForce< DIM >::SetWellWidth

(

double

wellWidth

)

Set mWellWidth.

Parameters

wellWidth

the new value of mWellWidth

Definition at line 203 of file ImmersedBoundaryMorseInteractionForce.cpp.

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 60 of file ImmersedBoundaryMorseInteractionForce.hpp.

Member Data Documentation

mLaminaRestLengthMult

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::mLaminaRestLengthMult

private

Multiplicative factor to change equilibrium length of interactions involving a lamina node. Initialised to 1.0 in constructor.

Definition at line 100 of file ImmersedBoundaryMorseInteractionForce.hpp.

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

mLaminaWellDepthMult

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::mLaminaWellDepthMult

private

Multiplicative factor to change strength of interactions involving a lamina node. Initialised to 1.0 in constructor.

Definition at line 94 of file ImmersedBoundaryMorseInteractionForce.hpp.

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

mRestLength

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::mRestLength

private

The basic rest length associated with interactions, as a fraction of cell population's interaction distance. Initialised to 0.25 in constructor.

Definition at line 88 of file ImmersedBoundaryMorseInteractionForce.hpp.

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

mWellDepth

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::mWellDepth

private

The basic interaction strength. Initialised to 1e3 in constructor.

Definition at line 82 of file ImmersedBoundaryMorseInteractionForce.hpp.

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

mWellWidth

template<unsigned DIM>

double ImmersedBoundaryMorseInteractionForce< DIM >::mWellWidth

private

The well width as a fraction of the cell population's interaction distance. Initialised to 0.25 in constructor.

Definition at line 106 of file ImmersedBoundaryMorseInteractionForce.hpp.

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

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

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