CryptProjectionForce Class Reference

#include <CryptProjectionForce.hpp>

Inheritance diagram for CryptProjectionForce:

Collaboration diagram for CryptProjectionForce:

List of all members.

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 (std::vector< c_vector< double, 2 > > &rForces, AbstractCellPopulation< 2 > &rCellPopulation)

void OutputForceParameters (out_stream &rParamsFile)

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

Detailed Description

A force law for use in crypt projection simulations.

Definition at line 39 of file CryptProjectionForce.hpp.

Constructor & Destructor Documentation

CryptProjectionForce::CryptProjectionForce ( )

Constructor.

Definition at line 33 of file CryptProjectionForce.cpp.

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

CryptProjectionForce::~CryptProjectionForce ( )

Destructor.

Definition at line 42 of file CryptProjectionForce.cpp.

Member Function Documentation

template<class Archive>

void CryptProjectionForce::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 47 of file CryptProjectionForce.hpp.

References mA, mB, mIncludeWntChemotaxis, and mWntChemotaxisStrength.

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 46 of file CryptProjectionForce.cpp.

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

Referenced by AddForceContribution().

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 108 of file CryptProjectionForce.cpp.

References CalculateCryptSurfaceDerivativeAtPoint(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), GeneralisedLinearSpringForce< 2 >::GetMeinekeSpringStiffness(), AbstractCellPopulation< DIM >::GetNode(), SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::IsMeshBasedCellPopulation(), AbstractTwoBodyInteractionForce< DIM >::mMechanicsCutOffLength, GeneralisedLinearSpringForce< 2 >::mMeinekeDivisionRestingSpringLength, GeneralisedLinearSpringForce< 2 >::mMeinekeSpringGrowthDuration, mNode3dLocationMap, AbstractTwoBodyInteractionForce< DIM >::mUseCutOffLength, and GeneralisedLinearSpringForce< 2 >::VariableSpringConstantMultiplicationFactor().

Referenced by AddForceContribution().

double CryptProjectionForce::GetA ( ) const

Returns:: mA.

Definition at line 73 of file CryptProjectionForce.cpp.

References mA.

double CryptProjectionForce::GetB ( ) const

Returns:: mB.

Definition at line 78 of file CryptProjectionForce.cpp.

References mB.

double CryptProjectionForce::GetWntChemotaxisStrength ( )

Returns:: mWntChemotaxisStrength

Definition at line 88 of file CryptProjectionForce.cpp.

References mWntChemotaxisStrength.

void CryptProjectionForce::SetWntChemotaxisStrength ( double wntChemotaxisStrength )

Set mWntChemotaxisStrength.

Parameters:

wntChemotaxisStrength

the new value of mWntChemotaxisStrength

Definition at line 83 of file CryptProjectionForce.cpp.

References mWntChemotaxisStrength.

void CryptProjectionForce::SetWntChemotaxis ( bool includeWntChemotaxis )

Set mIncludeWntChemotaxis.

Parameters:

includeWntChemotaxis

whether to include Wnt-dependent chemotaxis

Definition at line 93 of file CryptProjectionForce.cpp.

References mIncludeWntChemotaxis.

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 98 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by UpdateNode3dLocationMap().

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 103 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by CalculateForceBetweenNodes().

void CryptProjectionForce::AddForceContribution	(	std::vector< c_vector< double, 2 > > &	rForces,
		AbstractCellPopulation< 2 > &	rCellPopulation
	)

Overridden AddForceContribution method.

Parameters:

	rForces	reference to vector of forces on nodes
	rCellPopulation	reference to the cell population

Definition at line 244 of file CryptProjectionForce.cpp.

References AbstractCellPopulation< DIM >::Begin(), CalculateForceBetweenNodes(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::Instance(), AbstractCellPopulation< DIM >::IsMeshBasedCellPopulation(), mIncludeWntChemotaxis, mWntChemotaxisStrength, and UpdateNode3dLocationMap().

void CryptProjectionForce::OutputForceParameters ( out_stream & rParamsFile ) [virtual]

Outputs force parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 285 of file CryptProjectionForce.cpp.

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

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 45 of file CryptProjectionForce.hpp.

Member Data Documentation

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 62 of file CryptProjectionForce.hpp.

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

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 68 of file CryptProjectionForce.hpp.

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

bool CryptProjectionForce::mIncludeWntChemotaxis [private]

Whether to include Wnt-dependent chemotaxis for stem cells.

Definition at line 73 of file CryptProjectionForce.hpp.

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

double CryptProjectionForce::mWntChemotaxisStrength [private]

Strength of Wnt-based chemotactic force.

Definition at line 78 of file CryptProjectionForce.hpp.

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

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

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

Definition at line 83 of file CryptProjectionForce.hpp.

Referenced by CalculateForceBetweenNodes(), and UpdateNode3dLocationMap().

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

crypt/src/mechanics/CryptProjectionForce.hpp
crypt/src/mechanics/CryptProjectionForce.cpp


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 (std::vector< c_vector< double, 2 > > &rForces, AbstractCellPopulation< 2 > &rCellPopulation)
void	OutputForceParameters (out_stream &rParamsFile)
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