Chaste Release::3.1
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 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]
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().

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

Archive the object and its the member variables.

Parameters:
archivethe archive
versionthe 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:
numStepsthe 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:
sizeOfOdeSystemthe 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:
relTolthe relative tolerance for the solver
absTolthe 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:
pAbstractOdeSystempointer to the concrete ODE system to be solved
startTimethe time at which the initial conditions are specified
endTimethe time to which the system should be solved and the solution returned
timeStepthe 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.


Friends And Related Function Documentation

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

Member Data Documentation


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