#include <CryptProjectionForce.hpp>

Inheritance diagram for CryptProjectionForce:

Collaboration diagram for CryptProjectionForce:

Public Member Functions
	CryptProjectionForce ()

	~CryptProjectionForce ()

double	GetA () const

double	GetB () const

double	GetWntChemotaxisStrength ()

void	SetWntChemotaxisStrength (double wntChemotaxisStrength)

void	SetWntChemotaxis (bool includeWntChemotaxis)

double	CalculateCryptSurfaceHeightAtPoint (const c_vector< double, 2 > &rNodeLocation)

double	CalculateCryptSurfaceDerivativeAtPoint (const c_vector< double, 2 > &rNodeLocation)

void	AddForceContribution (AbstractCellPopulation< 2 > &rCellPopulation)

void	OutputForceParameters (out_stream &rParamsFile)

Public Member Functions inherited from GeneralisedLinearSpringForce< 2 >
	GeneralisedLinearSpringForce ()

virtual	~GeneralisedLinearSpringForce ()

virtual double	VariableSpringConstantMultiplicationFactor (unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation, bool isCloserThanRestLength)

c_vector< double, ELEMENT_DIM >	CalculateForceBetweenNodes (unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation)

double	GetMeinekeSpringStiffness ()

double	GetMeinekeDivisionRestingSpringLength ()

double	GetMeinekeSpringGrowthDuration ()

void	SetMeinekeSpringStiffness (double springStiffness)

void	SetMeinekeDivisionRestingSpringLength (double divisionRestingSpringLength)

void	SetMeinekeSpringGrowthDuration (double springGrowthDuration)

Public Member Functions inherited from AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >
	AbstractTwoBodyInteractionForce ()

bool	GetUseCutOffLength ()

void	SetCutOffLength (double cutOffLength)

double	GetCutOffLength ()

void	AddForceContribution (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

Public Member Functions inherited from AbstractForce< ELEMENT_DIM, SPACE_DIM >
	AbstractForce ()

virtual	~AbstractForce ()

void	OutputForceInfo (out_stream &rParamsFile)

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)

void	UpdateNode3dLocationMap (AbstractCellPopulation< 2 > &rCellPopulation)

c_vector< double, 2 >	CalculateForceBetweenNodes (unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< 2 > &rCellPopulation)

Private Attributes
double	mA

double	mB

bool	mIncludeWntChemotaxis

double	mWntChemotaxisStrength

std::map< unsigned, c_vector< double, 3 > >	mNode3dLocationMap

Friends
class	TestCryptProjectionForce

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from GeneralisedLinearSpringForce< 2 >
double	mMeinekeSpringStiffness

double	mMeinekeDivisionRestingSpringLength

double	mMeinekeSpringGrowthDuration

Protected Attributes inherited from AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >
bool	mUseCutOffLength

double	mMechanicsCutOffLength

Detailed Description

A force law for use in crypt projection simulations.

Definition at line 47 of file CryptProjectionForce.hpp.

Constructor & Destructor Documentation

◆ CryptProjectionForce()

CryptProjectionForce::CryptProjectionForce ( )

Constructor.

Definition at line 43 of file CryptProjectionForce.cpp.

References WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::GetCryptProjectionParameterB(), WntConcentration< DIM >::Instance(), mA, and mB.

◆ ~CryptProjectionForce()

CryptProjectionForce::~CryptProjectionForce ( )

Destructor.

Definition at line 52 of file CryptProjectionForce.cpp.

Member Function Documentation

◆ AddForceContribution()

void CryptProjectionForce::AddForceContribution ( AbstractCellPopulation< 2 > & rCellPopulation )

Overridden AddForceContribution method.

Parameters

rCellPopulation reference to the cell population

Definition at line 253 of file CryptProjectionForce.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), CalculateForceBetweenNodes(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::Instance(), mIncludeWntChemotaxis, mWntChemotaxisStrength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd(), and UpdateNode3dLocationMap().

◆ CalculateCryptSurfaceDerivativeAtPoint()

double CryptProjectionForce::CalculateCryptSurfaceDerivativeAtPoint ( const c_vector< double, 2 > & rNodeLocation )

Calculates the derivative df/dr of the crypt surface function z=f(r) at a point whose 2D position is a distance r from the centre of the cell_population, which we assume to be at (0,0).

Parameters

rNodeLocation the 2D location of a node

Returns: the gradient

Definition at line 113 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by CalculateForceBetweenNodes().

◆ CalculateCryptSurfaceHeightAtPoint()

double CryptProjectionForce::CalculateCryptSurfaceHeightAtPoint ( const c_vector< double, 2 > & rNodeLocation )

Calculates the height of the crypt surface given by z = f(r) = a*r^b at a point whose 2D position is a distance r from the centre of the cell population. This assumes that the cell population is centred at the origin.

Parameters

rNodeLocation

Returns: the z component corresponding to rNodeLocation

Definition at line 108 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by UpdateNode3dLocationMap().

◆ CalculateForceBetweenNodes()

c_vector< double, 2 > CryptProjectionForce::CalculateForceBetweenNodes	(	unsigned	nodeAGlobalIndex,
		unsigned	nodeBGlobalIndex,
		AbstractCellPopulation< 2 > &	rCellPopulation
	)

private

Calculates the force between two nodes.

Note that this assumes they are connected and is called by rCalculateVelocitiesOfEachNode()

Parameters

nodeAGlobalIndex	the index of the first node
nodeBGlobalIndex	the index of the second node
rCellPopulation	the cell population

Returns: The force exerted on Node A by Node B.

Definition at line 118 of file CryptProjectionForce.cpp.

References CalculateCryptSurfaceDerivativeAtPoint(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateCellPair(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), GeneralisedLinearSpringForce< 2 >::GetMeinekeSpringStiffness(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsMarkedSpring(), AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::mMechanicsCutOffLength, GeneralisedLinearSpringForce< 2 >::mMeinekeDivisionRestingSpringLength, GeneralisedLinearSpringForce< 2 >::mMeinekeSpringGrowthDuration, mNode3dLocationMap, AbstractTwoBodyInteractionForce< ELEMENT_DIM, SPACE_DIM >::mUseCutOffLength, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UnmarkSpring(), and GeneralisedLinearSpringForce< 2 >::VariableSpringConstantMultiplicationFactor().

Referenced by AddForceContribution().

◆ GetA()

double CryptProjectionForce::GetA ( ) const

Returns: mA.

Definition at line 83 of file CryptProjectionForce.cpp.

References mA.

◆ GetB()

double CryptProjectionForce::GetB ( ) const

Returns: mB.

Definition at line 88 of file CryptProjectionForce.cpp.

References mB.

◆ GetWntChemotaxisStrength()

double CryptProjectionForce::GetWntChemotaxisStrength ( )

Returns: mWntChemotaxisStrength

Definition at line 98 of file CryptProjectionForce.cpp.

References mWntChemotaxisStrength.

◆ OutputForceParameters()

void CryptProjectionForce::OutputForceParameters ( out_stream & rParamsFile )

virtual

Overridden OutputForceParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 298 of file CryptProjectionForce.cpp.

References mA, mB, mIncludeWntChemotaxis, mWntChemotaxisStrength, and GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::OutputForceParameters().

◆ serialize()

template<class Archive >

void CryptProjectionForce::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 62 of file CryptProjectionForce.hpp.

References mA, mB, mIncludeWntChemotaxis, and mWntChemotaxisStrength.

◆ SetWntChemotaxis()

void CryptProjectionForce::SetWntChemotaxis ( bool includeWntChemotaxis )

Set mIncludeWntChemotaxis.

Parameters

includeWntChemotaxis whether to include Wnt-dependent chemotaxis

Definition at line 103 of file CryptProjectionForce.cpp.

References mIncludeWntChemotaxis.

◆ SetWntChemotaxisStrength()

void CryptProjectionForce::SetWntChemotaxisStrength ( double wntChemotaxisStrength )

Set mWntChemotaxisStrength.

Parameters

wntChemotaxisStrength the new value of mWntChemotaxisStrength

Definition at line 93 of file CryptProjectionForce.cpp.

References mWntChemotaxisStrength.

◆ UpdateNode3dLocationMap()

void CryptProjectionForce::UpdateNode3dLocationMap ( AbstractCellPopulation< 2 > & rCellPopulation )

private

Fix up the mappings between node indices and 3D locations.

Parameters

rCellPopulation the cell population

Definition at line 56 of file CryptProjectionForce.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), CalculateCryptSurfaceHeightAtPoint(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), and mNode3dLocationMap.

Referenced by AddForceContribution().

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Definition at line 53 of file CryptProjectionForce.hpp.

◆ TestCryptProjectionForce

friend class TestCryptProjectionForce

friend

Definition at line 49 of file CryptProjectionForce.hpp.

Member Data Documentation

◆ mA

double CryptProjectionForce::mA

private

The value of the constant a in the definition of the crypt surface z = f(r) = a*r^b.

Definition at line 75 of file CryptProjectionForce.hpp.

Referenced by CryptProjectionForce(), CalculateCryptSurfaceDerivativeAtPoint(), CalculateCryptSurfaceHeightAtPoint(), GetA(), OutputForceParameters(), and serialize().

◆ mB

double CryptProjectionForce::mB

private

The value of the constant b in the definition of the crypt surface z = f(r) = a*r^b.

Definition at line 81 of file CryptProjectionForce.hpp.

Referenced by CryptProjectionForce(), CalculateCryptSurfaceDerivativeAtPoint(), CalculateCryptSurfaceHeightAtPoint(), GetB(), OutputForceParameters(), and serialize().

◆ mIncludeWntChemotaxis

bool CryptProjectionForce::mIncludeWntChemotaxis

private

Whether to include Wnt-dependent chemotaxis for stem cells.

Definition at line 86 of file CryptProjectionForce.hpp.

Referenced by AddForceContribution(), OutputForceParameters(), serialize(), and SetWntChemotaxis().

◆ mNode3dLocationMap

std::map<unsigned, c_vector<double, 3> > CryptProjectionForce::mNode3dLocationMap

private

Map node indices to 3D locations on the crypt surface.

Definition at line 96 of file CryptProjectionForce.hpp.

Referenced by CalculateForceBetweenNodes(), and UpdateNode3dLocationMap().

◆ mWntChemotaxisStrength

double CryptProjectionForce::mWntChemotaxisStrength

private

Strength of Wnt-based chemotactic force.

Definition at line 91 of file CryptProjectionForce.hpp.

Referenced by AddForceContribution(), GetWntChemotaxisStrength(), OutputForceParameters(), serialize(), and SetWntChemotaxisStrength().

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

crypt/src/forces/CryptProjectionForce.hpp
crypt/src/forces/CryptProjectionForce.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CryptProjectionForce()

◆ ~CryptProjectionForce()

Member Function Documentation

◆ AddForceContribution()

◆ CalculateCryptSurfaceDerivativeAtPoint()

◆ CalculateCryptSurfaceHeightAtPoint()

◆ CalculateForceBetweenNodes()

◆ GetA()

◆ GetB()

◆ GetWntChemotaxisStrength()

◆ OutputForceParameters()

◆ serialize()

◆ SetWntChemotaxis()

◆ SetWntChemotaxisStrength()

◆ UpdateNode3dLocationMap()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestCryptProjectionForce

Member Data Documentation

◆ mA

◆ mB

◆ mIncludeWntChemotaxis

◆ mNode3dLocationMap

◆ mWntChemotaxisStrength