Chaste Release::3.1
Public Member Functions | Private Member Functions | Private Attributes | Friends
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 deleteCellPopulationInDestructor=false, bool initialiseCells=true)
virtual ~CryptSimulation1d ()
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 55 of file CryptSimulation1d.hpp.

Constructor & Destructor Documentation

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

Constructor.

Parameters:
rCellPopulationA cell population object
deleteCellPopulationInDestructorWhether to delete the cell population on destruction to free up memory (defaults to false)
initialiseCellswhether to initialise cells (defaults to true, set to false when loading from an archive)

Definition at line 40 of file CryptSimulation1d.cpp.

References OffLatticeSimulation< 1 >::AddCellPopulationBoundaryCondition(), MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mDeleteCellPopulationInDestructor, mpStaticCastCellPopulation, and AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation.

CryptSimulation1d::~CryptSimulation1d ( ) [virtual]

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 57 of file CryptSimulation1d.cpp.

Member Function Documentation

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:
pParentCellthe parent cell
Returns:
daughter_coords the coordinates for the daughter cell.

Reimplemented from OffLatticeSimulation< 1 >.

Definition at line 61 of file CryptSimulation1d.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation(), RandomNumberGenerator::Instance(), mpStaticCastCellPopulation, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and RandomNumberGenerator::ranf().

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:
rParamsFilethe file stream to which the parameters are output

Reimplemented from OffLatticeSimulation< 1 >.

Definition at line 115 of file CryptSimulation1d.cpp.

template<class Archive >
void CryptSimulation1d::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the simulation and member variables.

Parameters:
archivethe archive
versionthe current version of this class

Reimplemented from OffLatticeSimulation< 1 >.

Definition at line 71 of file CryptSimulation1d.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from OffLatticeSimulation< 1 >.

Definition at line 63 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 80 of file CryptSimulation1d.hpp.

Referenced by CalculateCellDivisionVector(), and CryptSimulation1d().

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