#include <AbstractCellCycleModelOdeSolver.hpp>

Inheritance diagram for AbstractCellCycleModelOdeSolver:

Collaboration diagram for AbstractCellCycleModelOdeSolver:

Public Member Functions
	AbstractCellCycleModelOdeSolver ()
virtual	~AbstractCellCycleModelOdeSolver ()
virtual bool	IsSetUp ()=0
virtual void	Reset ()
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 40 of file AbstractCellCycleModelOdeSolver.cpp.

AbstractCellCycleModelOdeSolver::~AbstractCellCycleModelOdeSolver ( ) [virtual]

Virtual destructor since we have virtual methods.

Definition at line 45 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 84 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

unsigned AbstractCellCycleModelOdeSolver::GetSizeOfOdeSystem ( )

Returns:: mSizeOfOdeSystem

Definition at line 79 of file AbstractCellCycleModelOdeSolver.cpp.

References mSizeOfOdeSystem.

double AbstractCellCycleModelOdeSolver::GetStoppingTime ( )

Call mpOdeSolver->GetStoppingTime.

Returns:: mStoppingTime.

Definition at line 68 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

virtual void AbstractCellCycleModelOdeSolver::Initialise ( ) [pure virtual]

Initialise the ODE solver.

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

bool AbstractCellCycleModelOdeSolver::IsAdaptive ( ) [virtual]

Return 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 117 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

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

virtual bool AbstractCellCycleModelOdeSolver::IsSetUp ( ) [pure virtual]

Is the instance in existence and fully set up.

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

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

void AbstractCellCycleModelOdeSolver::Reset ( ) [virtual]

Reset the instance.

Reimplemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >.

Definition at line 49 of file AbstractCellCycleModelOdeSolver.cpp.

template<class Archive >

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

Archive the object and its the member variables.

Parameters:

archive	the archive
version	the current version of this class

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

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 95 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 74 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 106 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 53 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

bool AbstractCellCycleModelOdeSolver::StoppingEventOccurred ( )

Determine whether the solver quit due to the ODE's stopping event triggering

Definition at line 62 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.