CryptSimulation2d Class Reference

#include <CryptSimulation2d.hpp>

Collaboration diagram for CryptSimulation2d:

Public Member Functions
	CryptSimulation2d (AbstractTissue< 2 > &rTissue, std::vector< AbstractForce< 2 > * > forceCollection, bool deleteTissueAndForceCollection=false, bool initialiseCells=true)
void	UseJiggledBottomCells ()
void	ApplyTissueBoundaryConditions (const std::vector< c_vector< double, 2 > > &rOldLocations)
void	SetBottomCellAncestors ()
Protected Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
c_vector< double, 2 >	CalculateCellDivisionVector (TissueCell &rParentCell)
void	WriteVisualizerSetupFile ()
void	SetupWriteBetaCatenin ()
void	WriteBetaCatenin (double time)
void	SetupSolve ()
void	OutputParameters ()
void	PostSolve ()
void	AfterSolve ()
Protected Attributes
bool	mUseJiggledBottomCells
out_stream	mBetaCatResultsFile
MeshBasedTissueWithGhostNodes< 2 > *	mpStaticCastTissue
Friends
class	TestCryptSimulation2d
class	boost::serialization::access

Detailed Description

A 2D crypt simulation object. For more details, see the paper by van Leeuwen et al (2009) [doi:10.1111/j.1365-2184.2009.00627.x].

Definition at line 42 of file CryptSimulation2d.hpp.

Constructor & Destructor Documentation

CryptSimulation2d::CryptSimulation2d	(	AbstractTissue< 2 > &	rTissue,
		std::vector< AbstractForce< 2 > * >	forceCollection,
		bool	deleteTissueAndForceCollection = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters:

	rTissue	A tissue facade class (contains a mesh and cells)
	forceCollection	The mechanics to use in the simulation
	deleteTissueAndForceCollection	Whether to delete the tissue and force collection on destruction to free up memory
	initialiseCells	whether to initialise cells (set to false when loading from an archive)

Definition at line 35 of file CryptSimulation2d.cpp.

References mpStaticCastTissue, and TissueSimulation< 2 >::mrTissue.

Member Function Documentation

void CryptSimulation2d::AfterSolve ( ) [protected, virtual]

Overridden AfterSolve() method.

Closes beta catenin results file if required, then calls the base class method.

Reimplemented from TissueSimulation< 2 >.

Definition at line 250 of file CryptSimulation2d.cpp.

References mBetaCatResultsFile, and TissueSimulation< 2 >::mrTissue.

void CryptSimulation2d::ApplyTissueBoundaryConditions ( const std::vector< c_vector< double, 2 > > & rOldLocations )

Overridden ApplyTissueBoundaryConditions() method.

If an instance of WntConcentration is not set up, then stem cells at the bottom of the crypt are pinned. Any cell that has moved below the bottom of the crypt is moved back up.

Parameters:

rOldLocations

the node locations at the previous time step

If WntConcentration is not set up then stem cells must be pinned, so we reset the location of each stem cell.

Definition at line 266 of file CryptSimulation2d.cpp.

References AbstractTissue< DIM >::GetLocationIndexUsingCell(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), TissueSimulation< 2 >::mpRandomGenerator, mpStaticCastTissue, TissueSimulation< 2 >::mrTissue, mUseJiggledBottomCells, RandomNumberGenerator::ranf(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

c_vector< double, 2 > CryptSimulation2d::CalculateCellDivisionVector ( TissueCell & rParentCell ) [protected, virtual]

Calculates the new locations of a dividing cell's cell centres. Moves the dividing node a bit and returns co-ordinates for the new node. It does this by picking a random direction (0->2PI) and placing the parent and daughter in opposing directions on this axis.

Parameters:

rParentCell

the parent cell