#include <ImmersedBoundaryMorseMembraneForce.hpp>

Inheritance diagram for ImmersedBoundaryMorseMembraneForce< DIM >:

Collaboration diagram for ImmersedBoundaryMorseMembraneForce< DIM >:

Public Member Functions
	ImmersedBoundaryMorseMembraneForce ()

virtual	~ImmersedBoundaryMorseMembraneForce ()

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

void	OutputImmersedBoundaryForceParameters (out_stream &rParamsFile)

double	GetElementWellDepth () const

void	SetElementWellDepth (double elementWellDepth)

double	GetElementRestLength () const

void	SetElementRestLength (double elementRestLength)

double	GetLaminaWellDepth () const

void	SetLaminaWellDepth (double laminaWellDepth)

double	GetLaminaRestLength () const

void	SetLaminaRestLength (double laminaRestLength)

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)

template<unsigned ELEMENT_DIM>
void	CalculateForcesOnElement (ImmersedBoundaryElement< ELEMENT_DIM, DIM > &rElement, ImmersedBoundaryCellPopulation< DIM > &rCellPopulation, double intrinsicSpacingSquared)

Private Attributes
double	mElementWellDepth

double	mElementRestLength

double	mLaminaWellDepth

double	mLaminaRestLength

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 ImmersedBoundaryMorseMembraneForce< DIM >

A force class for use in immersed boundary simulations. This force implements Morse-potential-like links between adjacent nodes in each immersed boundary (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 53 of file ImmersedBoundaryMorseMembraneForce.hpp.

Constructor & Destructor Documentation

◆ ImmersedBoundaryMorseMembraneForce()

template<unsigned DIM>

ImmersedBoundaryMorseMembraneForce< DIM >::ImmersedBoundaryMorseMembraneForce ( )

Constructor

Definition at line 39 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ ~ImmersedBoundaryMorseMembraneForce()

template<unsigned DIM>

ImmersedBoundaryMorseMembraneForce< DIM >::~ImmersedBoundaryMorseMembraneForce ( )

virtual

Destructor

Definition at line 50 of file ImmersedBoundaryMorseMembraneForce.cpp.

Member Function Documentation

◆ AddImmersedBoundaryForceContribution()

template<unsigned DIM>

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

virtual

Overridden AddImmersedBoundaryForceContribution() method. Calculates basic elasticity in the membrane of each immersed boundary as a result of 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 55 of file ImmersedBoundaryMorseMembraneForce.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), ImmersedBoundaryCellPopulation< DIM >::GetIntrinsicSpacing(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetLaminaIteratorBegin(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetLaminaIteratorEnd(), and ImmersedBoundaryCellPopulation< DIM >::rGetMesh().

◆ CalculateForcesOnElement()

template<unsigned DIM>

template<unsigned ELEMENT_DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::CalculateForcesOnElement	(	ImmersedBoundaryElement< ELEMENT_DIM, DIM > &	rElement,
		ImmersedBoundaryCellPopulation< DIM > &	rCellPopulation,
		double	intrinsicSpacingSquared
	)

private

Helper method for AddImmersedBoundaryForceContribution. Calculates forces, and can accept either an element or a lamina

Template Parameters

ELEMENT_DIM either DIM or DIM-1 depending on whether receiving an element or a lamina

Parameters

rElement	the element or lamina add forces to
rCellPopulation	the immersed boundary cell population
intrinsicSpacingSquared	the square of the intrinsic spacing

Definition at line 86 of file ImmersedBoundaryMorseMembraneForce.cpp.

References ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetAverageNodeSpacingOfElement(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetAverageNodeSpacingOfLamina(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), and ImmersedBoundaryCellPopulation< DIM >::rGetMesh().

◆ GetElementRestLength()

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::GetElementRestLength ( ) const

Returns: mElementRestLength

Definition at line 190 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ GetElementWellDepth()

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::GetElementWellDepth ( ) const

Returns: mElementWellDepth

Definition at line 177 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ GetLaminaRestLength()

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::GetLaminaRestLength ( ) const

Returns: mLaminaRestLength

Definition at line 216 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ GetLaminaWellDepth()

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::GetLaminaWellDepth ( ) const

Returns: mLaminaWellDepth

Definition at line 203 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ GetWellWidth()

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::GetWellWidth ( ) const

Returns: mWellWidth

Definition at line 229 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ OutputImmersedBoundaryForceParameters()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< 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 163 of file ImmersedBoundaryMorseMembraneForce.cpp.

References AbstractImmersedBoundaryForce< DIM >::OutputImmersedBoundaryForceParameters().

◆ serialize()

template<unsigned DIM>

template<class Archive >

void ImmersedBoundaryMorseMembraneForce< 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 65 of file ImmersedBoundaryMorseMembraneForce.hpp.

References ImmersedBoundaryMorseMembraneForce< DIM >::mElementRestLength, ImmersedBoundaryMorseMembraneForce< DIM >::mElementWellDepth, ImmersedBoundaryMorseMembraneForce< DIM >::mLaminaRestLength, ImmersedBoundaryMorseMembraneForce< DIM >::mLaminaWellDepth, and ImmersedBoundaryMorseMembraneForce< DIM >::mWellWidth.

◆ SetElementRestLength()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::SetElementRestLength ( double elementRestLength )

Set mElementRestLength/

Parameters

elementRestLength the new value of mElementRestLength

Definition at line 196 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ SetElementWellDepth()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::SetElementWellDepth ( double elementWellDepth )

Set mElementWellDepth.

Parameters

elementWellDepth the new value of mElementWellDepth

Definition at line 183 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ SetLaminaRestLength()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::SetLaminaRestLength ( double laminaRestLength )

Set mLaminaRestLength/

Parameters

laminaRestLength the new value of mLaminaRestLength

Definition at line 222 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ SetLaminaWellDepth()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::SetLaminaWellDepth ( double laminaWellDepth )

Set mLaminaWellDepth.

Parameters

laminaWellDepth the new value of mLaminaWellDepth

Definition at line 209 of file ImmersedBoundaryMorseMembraneForce.cpp.

◆ SetWellWidth()

template<unsigned DIM>

void ImmersedBoundaryMorseMembraneForce< DIM >::SetWellWidth ( double wellWidth )

Set mWellWidth.

Parameters

wellWidth the new value of mWellWidth

Definition at line 235 of file ImmersedBoundaryMorseMembraneForce.cpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Definition at line 56 of file ImmersedBoundaryMorseMembraneForce.hpp.

Member Data Documentation

◆ mElementRestLength

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::mElementRestLength

private

The rest length associated with each element as a fraction of the average node spacing. Initialised to 0.5 in constructor.

Definition at line 84 of file ImmersedBoundaryMorseMembraneForce.hpp.

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

◆ mElementWellDepth

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::mElementWellDepth

private

The basic interaction strength. Initialised to 1e6 in constructor.

Definition at line 78 of file ImmersedBoundaryMorseMembraneForce.hpp.

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

◆ mLaminaRestLength

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::mLaminaRestLength

private

The rest length associated with each lamina as a fraction of the average node spacing. Initialised to 0.5 in constructor.

Definition at line 96 of file ImmersedBoundaryMorseMembraneForce.hpp.

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

◆ mLaminaWellDepth

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::mLaminaWellDepth

private

The spring constant associated with each lamina. Initialised to 1e6 in constructor.

Definition at line 90 of file ImmersedBoundaryMorseMembraneForce.hpp.

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

◆ mWellWidth

template<unsigned DIM>

double ImmersedBoundaryMorseMembraneForce< DIM >::mWellWidth

private

The well width as a fraction of the average node spacing in either an element or lamina. Initialised to 0.25 in constructor.

Definition at line 102 of file ImmersedBoundaryMorseMembraneForce.hpp.

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

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

cell_based/src/population/forces/ImmersedBoundaryMorseMembraneForce.hpp
cell_based/src/population/forces/ImmersedBoundaryMorseMembraneForce.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ImmersedBoundaryMorseMembraneForce()

◆ ~ImmersedBoundaryMorseMembraneForce()

Member Function Documentation

◆ AddImmersedBoundaryForceContribution()

◆ CalculateForcesOnElement()

◆ GetElementRestLength()

◆ GetElementWellDepth()

◆ GetLaminaRestLength()

◆ GetLaminaWellDepth()

◆ GetWellWidth()

◆ OutputImmersedBoundaryForceParameters()

◆ serialize()

◆ SetElementRestLength()

◆ SetElementWellDepth()

◆ SetLaminaRestLength()

◆ SetLaminaWellDepth()

◆ SetWellWidth()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mElementRestLength

◆ mElementWellDepth

◆ mLaminaRestLength

◆ mLaminaWellDepth

◆ mWellWidth