AbstractCellCycleModelOdeSolver Class Reference

#include <AbstractCellCycleModelOdeSolver.hpp>

Inheritance diagram for AbstractCellCycleModelOdeSolver:

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Collaboration diagram for AbstractCellCycleModelOdeSolver:

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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]

void AbstractCellCycleModelOdeSolver::Reset (  )  [virtual]

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]

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]


Member Data Documentation


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

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