#include <CryptSimulationBoundaryCondition.hpp>

Inheritance diagram for CryptSimulationBoundaryCondition< DIM >:

Collaboration diagram for CryptSimulationBoundaryCondition< DIM >:

Public Member Functions
	CryptSimulationBoundaryCondition (AbstractCellPopulation< DIM > *pCellPopulation)
void	ImposeBoundaryCondition (const std::vector< c_vector< double, DIM > > &rOldLocations)
bool	VerifyBoundaryCondition ()
void	SetUseJiggledBottomCells (bool useJiggledBottomCells)
bool	GetUseJiggledBottomCells ()
void	OutputCellPopulationBoundaryConditionParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
bool	mUseJiggledBottomCells
Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class CryptSimulationBoundaryCondition< DIM >

A boundary condition class for use with CryptSimulation2d, which pins stem cells in the absence of a Wnt stimulus, and optionally prevents cells moving below the y=0 boundary via random jiggling.

Definition at line 51 of file CryptSimulationBoundaryCondition.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CryptSimulationBoundaryCondition< DIM >::CryptSimulationBoundaryCondition ( AbstractCellPopulation< DIM > * pCellPopulation )

Constructor.

Parameters:

pCellPopulation pointer to the cell population

Definition at line 42 of file CryptSimulationBoundaryCondition.cpp.

Member Function Documentation

template<unsigned DIM>

bool CryptSimulationBoundaryCondition< DIM >::GetUseJiggledBottomCells ( )

Get method for mUseJiggledBottomCells.

Definition at line 193 of file CryptSimulationBoundaryCondition.cpp.

template<unsigned DIM>

void CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition ( const std::vector< c_vector< double, DIM > > & rOldLocations )

Overridden ImposeBoundaryCondition() method.

Apply the cell population boundary conditions.

Parameters:

rOldLocations the node locations before any boundary conditions are applied

Definition at line 49 of file CryptSimulationBoundaryCondition.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), WntConcentration< DIM >::Destroy(), RandomNumberGenerator::Instance(), WntConcentration< DIM >::Instance(), WntConcentration< DIM >::IsWntSetUp(), RandomNumberGenerator::ranf(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

template<unsigned DIM>

void CryptSimulationBoundaryCondition< DIM >::OutputCellPopulationBoundaryConditionParameters ( out_stream & rParamsFile ) [virtual]

Overridden OutputCellPopulationBoundaryConditionParameters() method. Output cell population boundary condition parameters to file.

Parameters:

rParamsFile the file stream to which the parameters are output

Todo:: Can we abstract these XML out methods and do automatic indentation?

Implements AbstractCellPopulationBoundaryCondition< DIM >.

Definition at line 199 of file CryptSimulationBoundaryCondition.cpp.

References AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationBoundaryConditionParameters().

template<unsigned DIM>

template<class Archive >

void CryptSimulationBoundaryCondition< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Serialize the object and its member variables.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractCellPopulationBoundaryCondition< DIM >.

Definition at line 70 of file CryptSimulationBoundaryCondition.hpp.

References CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells.

template<unsigned DIM>

void CryptSimulationBoundaryCondition< DIM >::SetUseJiggledBottomCells ( bool useJiggledBottomCells )

Set method for mUseJiggledBottomCells

Parameters:

useJiggledBottomCells whether to jiggle the cells on the bottom surface

Definition at line 187 of file CryptSimulationBoundaryCondition.cpp.

template<unsigned DIM>

bool CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition ( ) [virtual]

Overridden VerifyBoundaryCondition() method. Verify the boundary conditions have been applied. This is called after ImposeBoundaryCondition() to ensure the condition is still satisfied.