CryptSimulation1d Class Reference

#include <CryptSimulation1d.hpp>

Inheritance diagram for CryptSimulation1d:

Collaboration diagram for CryptSimulation1d:

List of all members.

Public Member Functions

CryptSimulation1d (AbstractCellPopulation< 1 > &rCellPopulation, bool deleteCellPopulationAndForceCollection=false, bool initialiseCells=true)

void ApplyCellPopulationBoundaryConditions (const std::vector< c_vector< double, 1 > > &rOldLocations)

void OutputSimulationParameters (out_stream &rParamsFile)

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

c_vector< double, 1 > CalculateCellDivisionVector (CellPtr pParentCell)

Private Attributes

MeshBasedCellPopulation< 1 > * mpStaticCastCellPopulation

Friends

class TestCryptSimulation1d

class boost::serialization::access

Detailed Description

A 1D crypt simulation object. The model is a simplified version of a 2D crypt model developed by Meineke et al (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 45 of file CryptSimulation1d.hpp.

Constructor & Destructor Documentation

CryptSimulation1d::CryptSimulation1d	(	AbstractCellPopulation< 1 > &	rCellPopulation,
		bool	deleteCellPopulationAndForceCollection = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters:

	rCellPopulation	A cell population object
	deleteCellPopulationAndForceCollection	Whether to delete the cell population 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 33 of file CryptSimulation1d.cpp.

References mpStaticCastCellPopulation, and CellBasedSimulation< 1 >::mrCellPopulation.

Member Function Documentation

template<class Archive>

void CryptSimulation1d::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the simulation and member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from CellBasedSimulation< 1 >.

Definition at line 61 of file CryptSimulation1d.hpp.

c_vector< double, 1 > CryptSimulation1d::CalculateCellDivisionVector ( CellPtr pParentCell ) [private, 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:

pParentCell

the parent cell

Returns:: daughter_coords the coordinates for the daughter cell.

Reimplemented from CellBasedSimulation< 1 >.

Definition at line 44 of file CryptSimulation1d.cpp.

References AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractCentreBasedCellPopulation< DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< DIM >::GetMeinekeDivisionSeparation(), RandomNumberGenerator::Instance(), mpStaticCastCellPopulation, CellBasedSimulation< 1 >::mrCellPopulation, and RandomNumberGenerator::ranf().

void CryptSimulation1d::ApplyCellPopulationBoundaryConditions ( const std::vector< c_vector< double, 1 > > & rOldLocations )

Overridden ApplyCellPopulationBoundaryConditions() 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 99 of file CryptSimulation1d.cpp.

References WntConcentration< DIM >::Destroy(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), WntConcentration< DIM >::Instance(), WntConcentration< DIM >::IsWntSetUp(), mpStaticCastCellPopulation, CellBasedSimulation< 1 >::mrCellPopulation, Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

void CryptSimulation1d::OutputSimulationParameters ( out_stream & rParamsFile ) [virtual]

Outputs simulation 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 CellBasedSimulation< 1 >.

Definition at line 144 of file CryptSimulation1d.cpp.

References CellBasedSimulation< DIM >::OutputSimulationParameters().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from CellBasedSimulation< 1 >.

Definition at line 53 of file CryptSimulation1d.hpp.

Member Data Documentation

MeshBasedCellPopulation<1>* CryptSimulation1d::mpStaticCastCellPopulation [private]

Helper member that is a static cast of the cell population.

Definition at line 69 of file CryptSimulation1d.hpp.

Referenced by ApplyCellPopulationBoundaryConditions(), CalculateCellDivisionVector(), and CryptSimulation1d().

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

crypt/src/simulation/CryptSimulation1d.hpp
crypt/src/simulation/CryptSimulation1d.cpp


Public Member Functions
	CryptSimulation1d (AbstractCellPopulation< 1 > &rCellPopulation, bool deleteCellPopulationAndForceCollection=false, bool initialiseCells=true)
void	ApplyCellPopulationBoundaryConditions (const std::vector< c_vector< double, 1 > > &rOldLocations)
void	OutputSimulationParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
c_vector< double, 1 >	CalculateCellDivisionVector (CellPtr pParentCell)
Private Attributes
MeshBasedCellPopulation< 1 > *	mpStaticCastCellPopulation
Friends
class	TestCryptSimulation1d
class	boost::serialization::access