CryptProjectionForce Class Reference

#include <CryptProjectionForce.hpp>

Inherits GeneralisedLinearSpringForce< 2 >.

Collaboration diagram for CryptProjectionForce:
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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 (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 47 of file CryptProjectionForce.hpp.

Constructor & Destructor Documentation

CryptProjectionForce::CryptProjectionForce (  ) 

Constructor.

Definition at line 41 of file CryptProjectionForce.cpp.

References mA, and mB.

CryptProjectionForce::~CryptProjectionForce (  ) 

Destructor.

Definition at line 50 of file CryptProjectionForce.cpp.

Member Function Documentation

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

Overridden AddForceContribution method.

Parameters:
rCellPopulation reference to the cell population

Definition at line 251 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(), mIncludeWntChemotaxis, mWntChemotaxisStrength, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsBegin(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringsEnd(), and 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 111 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by CalculateForceBetweenNodes().

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 106 of file CryptProjectionForce.cpp.

References mA, and mB.

Referenced by UpdateNode3dLocationMap().

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 116 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, ELEMENT_DIM >::mMechanicsCutOffLength, GeneralisedLinearSpringForce< 2 >::mMeinekeDivisionRestingSpringLength, GeneralisedLinearSpringForce< 2 >::mMeinekeSpringGrowthDuration, mNode3dLocationMap, AbstractTwoBodyInteractionForce< ELEMENT_DIM, ELEMENT_DIM >::mUseCutOffLength, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::UnmarkSpring(), and GeneralisedLinearSpringForce< 2 >::VariableSpringConstantMultiplicationFactor().

Referenced by AddForceContribution().

double CryptProjectionForce::GetA (  )  const
Returns:
mA.

Definition at line 81 of file CryptProjectionForce.cpp.

References mA.

double CryptProjectionForce::GetB (  )  const
Returns:
mB.

Definition at line 86 of file CryptProjectionForce.cpp.

References mB.

double CryptProjectionForce::GetWntChemotaxisStrength (  ) 
Returns:
mWntChemotaxisStrength

Definition at line 96 of file CryptProjectionForce.cpp.

References mWntChemotaxisStrength.

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 296 of file CryptProjectionForce.cpp.

References mA, mB, mIncludeWntChemotaxis, and mWntChemotaxisStrength.

template<class Archive >
void CryptProjectionForce::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

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.

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 62 of file CryptProjectionForce.hpp.

References mA, mB, mIncludeWntChemotaxis, and mWntChemotaxisStrength.

void CryptProjectionForce::SetWntChemotaxis ( bool  includeWntChemotaxis  ) 

Set mIncludeWntChemotaxis.

Parameters:
includeWntChemotaxis whether to include Wnt-dependent chemotaxis

Definition at line 101 of file CryptProjectionForce.cpp.

References mIncludeWntChemotaxis.

void CryptProjectionForce::SetWntChemotaxisStrength ( double  wntChemotaxisStrength  ) 

Set mWntChemotaxisStrength.

Parameters:
wntChemotaxisStrength the new value of mWntChemotaxisStrength

Definition at line 91 of file CryptProjectionForce.cpp.

References 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 54 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 Function Documentation

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

Needed for serialization.

Reimplemented from GeneralisedLinearSpringForce< 2 >.

Definition at line 53 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 75 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 81 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 86 of file CryptProjectionForce.hpp.

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

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().

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().

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