#include <CryptSimulationBoundaryCondition.hpp>

Inheritance diagram for CryptSimulationBoundaryCondition< DIM >:

Collaboration diagram for CryptSimulationBoundaryCondition< DIM >:

Public Member Functions
	CryptSimulationBoundaryCondition (AbstractCellPopulation< DIM > *pCellPopulation)

void	ImposeBoundaryCondition (const std::map< Node< DIM > *, c_vector< double, DIM > > &rOldLocations)

bool	VerifyBoundaryCondition ()

void	SetUseJiggledBottomCells (bool useJiggledBottomCells)

bool	GetUseJiggledBottomCells ()

void	OutputCellPopulationBoundaryConditionParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractCellPopulationBoundaryCondition< DIM >
	AbstractCellPopulationBoundaryCondition (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > *pCellPopulation)

virtual	~AbstractCellPopulationBoundaryCondition ()

virtual void	ImposeBoundaryCondition (const std::map< Node< ELEMENT_DIM > *, c_vector< double, ELEMENT_DIM > > &rOldLocations)=0

const AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > *	GetCellPopulation () const

void	OutputCellPopulationBoundaryConditionInfo (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)

Private Attributes
bool	mUseJiggledBottomCells

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractCellPopulationBoundaryCondition< DIM >
AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > *	mpCellPopulation

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 43 of file CryptSimulationBoundaryCondition.cpp.

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

Member Function Documentation

template<unsigned DIM>

bool CryptSimulationBoundaryCondition< DIM >::GetUseJiggledBottomCells ( )

Returns: mUseJiggledBottomCells.

Definition at line 194 of file CryptSimulationBoundaryCondition.cpp.

References CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells.

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

template<unsigned DIM>

void CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition ( const std::map< Node< DIM > *, 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 50 of file CryptSimulationBoundaryCondition.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), WntConcentration< DIM >::Destroy(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), WntConcentration< DIM >::Instance(), RandomNumberGenerator::Instance(), WntConcentration< DIM >::IsWntSetUp(), AbstractCellPopulationBoundaryCondition< DIM >::mpCellPopulation, CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells, RandomNumberGenerator::ranf(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

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

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 200 of file CryptSimulationBoundaryCondition.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells, and AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationBoundaryConditionParameters().

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

template<unsigned DIM>

template<class Archive >

void CryptSimulationBoundaryCondition< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 70 of file CryptSimulationBoundaryCondition.hpp.

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 188 of file CryptSimulationBoundaryCondition.cpp.

References CryptSimulationBoundaryCondition< DIM >::mUseJiggledBottomCells.

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

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.