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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractCellCycleModelOdeSolver.hpp>
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 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 |
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.
AbstractCellCycleModelOdeSolver::AbstractCellCycleModelOdeSolver | ( | ) |
Constructor.
Definition at line 39 of file AbstractCellCycleModelOdeSolver.cpp.
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virtual |
Virtual destructor since we have virtual methods.
Definition at line 44 of file AbstractCellCycleModelOdeSolver.cpp.
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 CheckForStoppingEvents(), IsSetUp(), and mpOdeSolver.
Referenced by CheckForStoppingEvents().
unsigned AbstractCellCycleModelOdeSolver::GetSizeOfOdeSystem | ( | ) |
Definition at line 74 of file AbstractCellCycleModelOdeSolver.cpp.
References mSizeOfOdeSystem.
double AbstractCellCycleModelOdeSolver::GetStoppingTime | ( | ) |
Call mpOdeSolver->GetStoppingTime.
Definition at line 63 of file AbstractCellCycleModelOdeSolver.cpp.
References IsSetUp(), and mpOdeSolver.
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pure virtual |
Initialise the ODE solver.
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >.
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virtual |
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().
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pure virtual |
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >.
Referenced by CheckForStoppingEvents(), GetStoppingTime(), IsAdaptive(), SetMaxSteps(), SetTolerances(), SolveAndUpdateStateVariable(), and StoppingEventOccurred().
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pure virtual |
Reset the instance.
As this method is pure virtual, it must be overridden in subclasses.
Implemented in CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >, and CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >.
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inlineprivate |
Archive the object and its the member variables.
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 | 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).
numSteps | the new maximum number of steps |
Definition at line 90 of file AbstractCellCycleModelOdeSolver.cpp.
References IsSetUp(), mpOdeSolver, and SetMaxSteps().
Referenced by SetMaxSteps().
void AbstractCellCycleModelOdeSolver::SetSizeOfOdeSystem | ( | unsigned | sizeOfOdeSystem | ) |
Set method for mSizeOfOdeSystem.
sizeOfOdeSystem | the new value of mSizeOfOdeSystem |
Definition at line 69 of file AbstractCellCycleModelOdeSolver.cpp.
References mSizeOfOdeSystem.
If using CVODE, set relative and absolute tolerances; both scalars. If no parameters are given, tolerances will be reset to default values.
relTol | the relative tolerance for the solver |
absTol | the absolute tolerance for the solver |
Definition at line 101 of file AbstractCellCycleModelOdeSolver.cpp.
References IsSetUp(), mpOdeSolver, and SetTolerances().
Referenced by SetTolerances().
void AbstractCellCycleModelOdeSolver::SolveAndUpdateStateVariable | ( | AbstractOdeSystem * | pAbstractOdeSystem, |
double | startTime, | ||
double | endTime, | ||
double | timeStep | ||
) |
Call mpOdeSolver->SolveAndUpdateStateVariable.
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 | ( | ) |
Definition at line 57 of file AbstractCellCycleModelOdeSolver.cpp.
References IsSetUp(), and mpOdeSolver.
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friend |
Needed for serialization.
Definition at line 61 of file AbstractCellCycleModelOdeSolver.hpp.
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protected |
The ODE solver.
Definition at line 78 of file AbstractCellCycleModelOdeSolver.hpp.
Referenced by CheckForStoppingEvents(), GetStoppingTime(), IsAdaptive(), serialize(), SetMaxSteps(), SetTolerances(), SolveAndUpdateStateVariable(), and StoppingEventOccurred().
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protected |
The size of the ODE system to be solved.
Definition at line 81 of file AbstractCellCycleModelOdeSolver.hpp.
Referenced by GetSizeOfOdeSystem(), serialize(), and SetSizeOfOdeSystem().