AbstractCellCycleModelOdeSolver Class Reference

#include <AbstractCellCycleModelOdeSolver.hpp>

Inheritance diagram for AbstractCellCycleModelOdeSolver:

Collaboration diagram for AbstractCellCycleModelOdeSolver:

List of all members.

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 49 of file AbstractCellCycleModelOdeSolver.hpp.

Constructor & Destructor Documentation

AbstractCellCycleModelOdeSolver::AbstractCellCycleModelOdeSolver ( )

Constructor.

Definition at line 33 of file AbstractCellCycleModelOdeSolver.cpp.

AbstractCellCycleModelOdeSolver::~AbstractCellCycleModelOdeSolver ( ) [virtual]

Virtual destructor since we have virtual methods.

Definition at line 38 of file AbstractCellCycleModelOdeSolver.cpp.

Member Function Documentation

template<class Archive>

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

Archive the member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

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 67 of file AbstractCellCycleModelOdeSolver.hpp.

References mpOdeSolver, and mSizeOfOdeSystem.

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 42 of file AbstractCellCycleModelOdeSolver.cpp.

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 46 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::StoppingEventOccurred ( )

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

Definition at line 55 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

double AbstractCellCycleModelOdeSolver::GetStoppingTime ( )

Call mpOdeSolver->GetStoppingTime.

Returns:: mStoppingTime.

Definition at line 61 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 67 of file AbstractCellCycleModelOdeSolver.cpp.

References mSizeOfOdeSystem.

unsigned AbstractCellCycleModelOdeSolver::GetSizeOfOdeSystem ( )

Returns:: mSizeOfOdeSystem

Definition at line 72 of file AbstractCellCycleModelOdeSolver.cpp.

References mSizeOfOdeSystem.

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 77 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

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 88 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

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 99 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

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 110 of file AbstractCellCycleModelOdeSolver.cpp.

References IsSetUp(), and mpOdeSolver.

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

Friends And Related Function Documentation

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

Needed for serialization.

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

Definition at line 54 of file AbstractCellCycleModelOdeSolver.hpp.

Member Data Documentation

boost::shared_ptr<AbstractIvpOdeSolver> AbstractCellCycleModelOdeSolver::mpOdeSolver [protected]

The ODE solver.

Definition at line 76 of file AbstractCellCycleModelOdeSolver.hpp.

Referenced by CheckForStoppingEvents(), GetStoppingTime(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Initialise(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Initialise(), IsAdaptive(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::IsSetUp(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::IsSetUp(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Reset(), serialize(), SetMaxSteps(), SetTolerances(), SolveAndUpdateStateVariable(), and StoppingEventOccurred().

unsigned AbstractCellCycleModelOdeSolver::mSizeOfOdeSystem [protected]

The size of the ODE system to be solved.

Definition at line 79 of file AbstractCellCycleModelOdeSolver.hpp.

Referenced by GetSizeOfOdeSystem(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Initialise(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::IsSetUp(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Reset(), serialize(), and SetSizeOfOdeSystem().

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

cell_based/src/population/cell/cycle/AbstractCellCycleModelOdeSolver.hpp
cell_based/src/population/cell/cycle/AbstractCellCycleModelOdeSolver.cpp


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