CvodeAdaptor Class Reference

#include <CvodeAdaptor.hpp>

Inheritance diagram for CvodeAdaptor:

Collaboration diagram for CvodeAdaptor:

List of all members.

Public Member Functions

CvodeAdaptor (double relTol=1e-4, double absTol=1e-6)

void SetTolerances (double relTol=1e-4, double absTol=1e-6)

double GetRelativeTolerance ()

double GetAbsoluteTolerance ()

double GetLastStepSize ()

OdeSolution Solve (AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep, double timeSampling)

void Solve (AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep)

void CheckForStoppingEvents ()

void SetMaxSteps (long int numSteps)

long int GetMaxSteps ()

Protected Member Functions

void SetupCvode (AbstractOdeSystem *pOdeSystem, std::vector< double > &rInitialY, double startTime, double maxStep)

void FreeCvodeMemory ()

void CvodeError (int flag, const char *msg)

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Private Attributes

void * mpCvodeMem

N_Vector mInitialValues

CvodeData mData

double mRelTol

double mAbsTol

double mLastInternalStepSize

long int mMaxSteps

bool mCheckForRoots

Friends

class boost::serialization::access

Detailed Description

The CVODE adaptor ODE solver class.

Assumes that it will be solving stiff systems, so uses BDF/Newton.

The timeStep parameters of the abstract class are here used to specify *maximum* steps, since the solver is adaptive.

Note that a call to Solve will initialise the CVODE solver, and free its working memory when done. There is thus a non-trivial overhead involved.

Todo:: Add an option to just initialise once, and assume subsequent Solve calls are continuing from where we left off.

Definition at line 82 of file CvodeAdaptor.hpp.

Constructor & Destructor Documentation

CvodeAdaptor::CvodeAdaptor	(	double	relTol = `1e-4`,
		double	absTol = `1e-6`
	)

Default constructor. Can optionally set relative and absolute tolerances.

Parameters:

	relTol	the relative tolerance for the solver
	absTol	the absolute tolerance for the solver

Definition at line 352 of file CvodeAdaptor.cpp.

Member Function Documentation

template<class Archive>

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

Archive, never used directly - boost uses this.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractIvpOdeSolver.

Definition at line 94 of file CvodeAdaptor.hpp.

References mAbsTol, mCheckForRoots, mLastInternalStepSize, mMaxSteps, and mRelTol.

void CvodeAdaptor::SetupCvode	(	AbstractOdeSystem *	pOdeSystem,
		std::vector< double > &	rInitialY,
		double	startTime,
		double	maxStep
	)			`[protected]`

Set up the CVODE data structures needed to solve the given system.

Parameters:

	pOdeSystem	the ODE system being solved
	rInitialY	initial conditions vector
	startTime	when to simulate from
	maxStep	maximum time step

Definition at line 173 of file CvodeAdaptor.cpp.

References EXCEPTION, AbstractParameterisedSystem< VECTOR >::GetNumberOfStateVariables(), mAbsTol, mCheckForRoots, mData, mInitialValues, mMaxSteps, mpCvodeMem, mRelTol, CvodeData_::pSystem, and CvodeData_::pY.

Referenced by Solve().

void CvodeAdaptor::FreeCvodeMemory ( ) [protected]

Free CVODE memory after solving a system of ODEs.

Definition at line 226 of file CvodeAdaptor.cpp.

References mInitialValues, and mpCvodeMem.

Referenced by Solve().

void CvodeAdaptor::CvodeError	(	int	flag,
		const char *	msg
	)			`[protected]`

Report an error from CVODE.

This will (probably) never be called, since we supply an error handler function which throws an exception.

Parameters:

	flag	error flag
	msg	error message

Definition at line 238 of file CvodeAdaptor.cpp.

References EXCEPTION.

Referenced by Solve().

void CvodeAdaptor::SetTolerances	(	double	relTol = `1e-4`,
		double	absTol = `1e-6`
	)

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 362 of file CvodeAdaptor.cpp.

References mAbsTol, and mRelTol.

double CvodeAdaptor::GetRelativeTolerance ( )

Get the relative tolerance.

Definition at line 368 of file CvodeAdaptor.cpp.

References mRelTol.

double CvodeAdaptor::GetAbsoluteTolerance ( )

Get the absolute tolerance.

Definition at line 373 of file CvodeAdaptor.cpp.

References mAbsTol.

double CvodeAdaptor::GetLastStepSize ( )

Get the last step size used internally by CVODE in the last Solve call

Definition at line 378 of file CvodeAdaptor.cpp.

References mLastInternalStepSize.

OdeSolution CvodeAdaptor::Solve	(	AbstractOdeSystem *	pOdeSystem,
		std::vector< double > &	rYValues,
		double	startTime,
		double	endTime,
		double	maxStep,
		double	timeSampling
	)			`[virtual]`

Solve the given ODE system, returning the solution at sampling intervals.

Parameters:

	pOdeSystem	the ODE system to solve
	rYValues	the initial state variable values (note: this vector will also be used as working memory)
	startTime	the time to start solving at
	endTime	the time to solve to
	maxStep	the maximum time step to be taken by the adaptive solver
	timeSampling	the interval at which to sample the solution

Returns:: the solution

Implements AbstractIvpOdeSolver.

Definition at line 249 of file CvodeAdaptor.cpp.

References TimeStepper::AdvanceOneTimeStep(), AbstractOdeSystem::CalculateStoppingEvent(), CvodeError(), TimeStepper::EstimateTimeSteps(), EXCEPTION, FreeCvodeMemory(), TimeStepper::GetNextTime(), AbstractParameterisedSystem< VECTOR >::GetSystemInformation(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), mCheckForRoots, mInitialValues, mLastInternalStepSize, mpCvodeMem, AbstractIvpOdeSolver::mStoppingEventOccurred, AbstractIvpOdeSolver::mStoppingTime, OdeSolution::rGetSolutions(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), and SetupCvode().

void CvodeAdaptor::Solve	(	AbstractOdeSystem *	pOdeSystem,
		std::vector< double > &	rYValues,
		double	startTime,
		double	endTime,
		double	maxStep
	)			`[virtual]`

Solve the given ODE system, storing the final result in rYValues.

Parameters:

	pOdeSystem	the ODE system to solve
	rYValues	the initial state variable values; will be filled in with the final values on return
	startTime	the time to start solving at
	endTime	the time to solve to
	maxStep	the maximum time step to be taken by the adaptive solver

Implements AbstractIvpOdeSolver.

Definition at line 310 of file CvodeAdaptor.cpp.

References AbstractOdeSystem::CalculateStoppingEvent(), CvodeError(), EXCEPTION, FreeCvodeMemory(), mCheckForRoots, mInitialValues, mLastInternalStepSize, mpCvodeMem, AbstractIvpOdeSolver::mStoppingEventOccurred, AbstractIvpOdeSolver::mStoppingTime, and SetupCvode().

void CvodeAdaptor::CheckForStoppingEvents ( )

Make the solver check for stopping events using CVODE's rootfinding functionality.

By default we do not check.

Definition at line 383 of file CvodeAdaptor.cpp.

References mCheckForRoots.

void CvodeAdaptor::SetMaxSteps ( long int numSteps )

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

new maximum number of steps

Definition at line 388 of file CvodeAdaptor.cpp.

References mMaxSteps.

long int CvodeAdaptor::GetMaxSteps ( )

Get the maximum number of steps to be taken by the solver in its attempt to reach the next output time.

Definition at line 393 of file CvodeAdaptor.cpp.

References mMaxSteps.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractIvpOdeSolver.

Definition at line 86 of file CvodeAdaptor.hpp.

Member Data Documentation

void* CvodeAdaptor::mpCvodeMem [private]

Pointer to the CVODE memory block.

Definition at line 106 of file CvodeAdaptor.hpp.

Referenced by FreeCvodeMemory(), SetupCvode(), and Solve().

N_Vector CvodeAdaptor::mInitialValues [private]

Initial conditions for the ODE solver.

Definition at line 109 of file CvodeAdaptor.hpp.

Referenced by FreeCvodeMemory(), SetupCvode(), and Solve().

CvodeData CvodeAdaptor::mData [private]

The CVODE data structure.

Definition at line 112 of file CvodeAdaptor.hpp.

Referenced by SetupCvode().

double CvodeAdaptor::mRelTol [private]

Relative tolerance for the ODE solver.

Definition at line 115 of file CvodeAdaptor.hpp.

Referenced by GetRelativeTolerance(), serialize(), SetTolerances(), and SetupCvode().

double CvodeAdaptor::mAbsTol [private]

Absolute tolerance for the ODE solver.

Definition at line 118 of file CvodeAdaptor.hpp.

Referenced by GetAbsoluteTolerance(), serialize(), SetTolerances(), and SetupCvode().

double CvodeAdaptor::mLastInternalStepSize [private]

The size of the previous timestep.

Definition at line 121 of file CvodeAdaptor.hpp.

Referenced by GetLastStepSize(), serialize(), and Solve().

long int CvodeAdaptor::mMaxSteps [private]

The maximum number of steps to be taken by the solver in its attempt to reach the next output time.

Definition at line 127 of file CvodeAdaptor.hpp.

Referenced by GetMaxSteps(), serialize(), SetMaxSteps(), and SetupCvode().

bool CvodeAdaptor::mCheckForRoots [private]

Whether to check for stopping events.

Definition at line 130 of file CvodeAdaptor.hpp.

Referenced by CheckForStoppingEvents(), serialize(), SetupCvode(), and Solve().

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

ode/src/solver/CvodeAdaptor.hpp
ode/src/solver/CvodeAdaptor.cpp


Public Member Functions
	CvodeAdaptor (double relTol=1e-4, double absTol=1e-6)
void	SetTolerances (double relTol=1e-4, double absTol=1e-6)
double	GetRelativeTolerance ()
double	GetAbsoluteTolerance ()
double	GetLastStepSize ()
OdeSolution	Solve (AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep, double timeSampling)
void	Solve (AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep)
void	CheckForStoppingEvents ()
void	SetMaxSteps (long int numSteps)
long int	GetMaxSteps ()
Protected Member Functions
void	SetupCvode (AbstractOdeSystem *pOdeSystem, std::vector< double > &rInitialY, double startTime, double maxStep)
void	FreeCvodeMemory ()
void	CvodeError (int flag, const char *msg)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
void *	mpCvodeMem
N_Vector	mInitialValues
CvodeData	mData
double	mRelTol
double	mAbsTol
double	mLastInternalStepSize
long int	mMaxSteps
bool	mCheckForRoots
Friends
class	boost::serialization::access