#include <AbstractCellCycleModelOdeSolver.hpp>

Inheritance diagram for AbstractCellCycleModelOdeSolver:

Collaboration diagram for AbstractCellCycleModelOdeSolver:

Public Member Functions
	AbstractCellCycleModelOdeSolver ()

virtual	~AbstractCellCycleModelOdeSolver ()

virtual bool	IsSetUp ()=0

virtual void	Reset ()=0

void	SolveAndUpdateStateVariable (AbstractOdeSystem *pAbstractOdeSystem, double startTime, double endTime, double timeStep)

virtual void	Initialise ()=0

bool	StoppingEventOccurred ()

double	GetStoppingTime ()

void	SetSizeOfOdeSystem (unsigned sizeOfOdeSystem)

unsigned	GetSizeOfOdeSystem ()

void	CheckForStoppingEvents ()

void	SetMaxSteps (long int numSteps)

void	SetTolerances (double relTol=1e-4, double absTol=1e-6)

virtual bool	IsAdaptive ()

Protected Attributes
boost::shared_ptr < AbstractIvpOdeSolver >	mpOdeSolver

unsigned	mSizeOfOdeSystem

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Detailed Description

This provides a wrapper around any ODE solver class, exposing roughly the same interface, for use by ODE-based cell-cycle models. Its main purpose is to allow multiple instances of the same cell-cycle model to share the same ODE solver instance.

The recommended way to use this wrapper is via the CellCycleModelOdeSolver subclass, which is templated over cell-cycle model class and ODE solver class, providing a singleton instance for each combination of template parameters.

Definition at line 56 of file AbstractCellCycleModelOdeSolver.hpp.

Constructor & Destructor Documentation

AbstractCellCycleModelOdeSolver::AbstractCellCycleModelOdeSolver ( )

Constructor.

Definition at line 39 of file AbstractCellCycleModelOdeSolver.cpp.

AbstractCellCycleModelOdeSolver::~AbstractCellCycleModelOdeSolver ( )

virtual

Virtual destructor since we have virtual methods.

Definition at line 44 of file AbstractCellCycleModelOdeSolver.cpp.

Member Function Documentation

void AbstractCellCycleModelOdeSolver::CheckForStoppingEvents ( )

If using CVODE, make the solver check for stopping events using CVODE's rootfinding functionality (by default we do not check).

Definition at line 79 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

unsigned AbstractCellCycleModelOdeSolver::GetSizeOfOdeSystem ( )

Returns: mSizeOfOdeSystem

Definition at line 74 of file AbstractCellCycleModelOdeSolver.cpp.

References mSizeOfOdeSystem.

double AbstractCellCycleModelOdeSolver::GetStoppingTime ( )

Call mpOdeSolver->GetStoppingTime.

Returns: mStoppingTime.

Definition at line 63 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

virtual void AbstractCellCycleModelOdeSolver::Initialise ( )

pure virtual

Initialise the ODE solver.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >.

bool AbstractCellCycleModelOdeSolver::IsAdaptive ( )

virtual

Returns: true iff this is an adaptive solver such as CVODE for which it is safe to set the 'timestep' to be the outer simulation timestep, because the ODE solver will use this as its maximum, not actual, timestep.

The base class version just returns true iff the solver is the CvodeAdaptor class.

Reimplemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >.

Definition at line 112 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

Referenced by CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::IsAdaptive().

virtual bool AbstractCellCycleModelOdeSolver::IsSetUp ( )

pure virtual

Returns: whether the instance in existence and fully set up.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >.

Referenced by CheckForStoppingEvents(), GetStoppingTime(), IsAdaptive(), SetMaxSteps(), SetTolerances(), SolveAndUpdateStateVariable(), and StoppingEventOccurred().

virtual void AbstractCellCycleModelOdeSolver::Reset ( )

pure virtual

Reset the instance.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >.

template<class Archive >

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

inlineprivate

Archive the object and its the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 69 of file AbstractCellCycleModelOdeSolver.hpp.

References mpOdeSolver, and mSizeOfOdeSystem.

void AbstractCellCycleModelOdeSolver::SetMaxSteps ( long int numSteps )

If using CVODE, change the maximum number of steps to be taken by the solver in its attempt to reach the next output time (default is 500).

Parameters

numSteps the new maximum number of steps

Definition at line 90 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

void AbstractCellCycleModelOdeSolver::SetSizeOfOdeSystem ( unsigned sizeOfOdeSystem )

Set method for mSizeOfOdeSystem.

Parameters

sizeOfOdeSystem the new value of mSizeOfOdeSystem

Definition at line 69 of file AbstractCellCycleModelOdeSolver.cpp.

References mSizeOfOdeSystem.

void AbstractCellCycleModelOdeSolver::SetTolerances	(	double	relTol = `1e-4`,
		double	absTol = `1e-6`
	)

If using CVODE, set relative and absolute tolerances; both scalars. If no parameters are given, tolerances will be reset to default values.

Parameters

relTol	the relative tolerance for the solver
absTol	the absolute tolerance for the solver

Definition at line 101 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

void AbstractCellCycleModelOdeSolver::SolveAndUpdateStateVariable	(	AbstractOdeSystem *	pAbstractOdeSystem,
		double	startTime,
		double	endTime,
		double	timeStep
	)

Call mpOdeSolver->SolveAndUpdateStateVariable.

Parameters

pAbstractOdeSystem	pointer to the concrete ODE system to be solved
startTime	the time at which the initial conditions are specified
endTime	the time to which the system should be solved and the solution returned
timeStep	the time interval to be used by the solver

Definition at line 48 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

bool AbstractCellCycleModelOdeSolver::StoppingEventOccurred ( )