#include <CvodeAdaptor.hpp>

Inheritance diagram for CvodeAdaptor:

Collaboration diagram for CvodeAdaptor:

Public Member Functions
	CvodeAdaptor (double relTol=1e-4, double absTol=1e-6)
	~CvodeAdaptor ()
void	SetTolerances (double relTol=1e-4, double absTol=1e-6)
double	GetRelativeTolerance ()
double	GetAbsoluteTolerance ()
double	GetLastStepSize ()
void	SetAutoReset (bool autoReset)
void	SetMinimalReset (bool minimalReset)
void	ResetSolver ()
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)
void	RecordStoppingPoint (double stopTime, N_Vector yEnd)
Private Attributes
void *	mpCvodeMem
CvodeData	mData
double	mRelTol
double	mAbsTol
double	mLastInternalStepSize
long int	mMaxSteps
bool	mCheckForRoots
N_Vector	mLastSolutionState
double	mLastSolutionTime
bool	mAutoReset
bool	mForceMinimalReset
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 89 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 435 of file CvodeAdaptor.cpp.

CvodeAdaptor::~CvodeAdaptor ( )

Destructor. Frees memory.

Definition at line 450 of file CvodeAdaptor.cpp.

References DeleteVector(), FreeCvodeMemory(), and mLastSolutionState.

Member Function Documentation

void CvodeAdaptor::CheckForStoppingEvents ( )

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

By default we do not check.

Definition at line 491 of file CvodeAdaptor.cpp.

References mCheckForRoots.

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 317 of file CvodeAdaptor.cpp.

References EXCEPTION.

Referenced by Solve().

void CvodeAdaptor::FreeCvodeMemory ( ) [protected]

Free CVODE memory after solving a system of ODEs.

Definition at line 282 of file CvodeAdaptor.cpp.

References mpCvodeMem.

Referenced by Solve(), and ~CvodeAdaptor().

double CvodeAdaptor::GetAbsoluteTolerance ( )

Get the absolute tolerance.

Definition at line 481 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 486 of file CvodeAdaptor.cpp.

References mLastInternalStepSize.

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 501 of file CvodeAdaptor.cpp.

References mMaxSteps.

double CvodeAdaptor::GetRelativeTolerance ( )

Get the relative tolerance.

Definition at line 476 of file CvodeAdaptor.cpp.

References mRelTol.

void CvodeAdaptor::RecordStoppingPoint	(	double	stopTime,
		N_Vector	yEnd
	)		`[private]`

Record where the last solve got to so we know whether to re-initialise.

Parameters:

stopTime	the finishing time
yEnd	the state variables at this time

Definition at line 456 of file CvodeAdaptor.cpp.

References CreateVectorIfEmpty(), GetVectorComponent(), GetVectorSize(), mAutoReset, mLastSolutionState, mLastSolutionTime, and SetVectorComponent().

Referenced by Solve().

void CvodeAdaptor::ResetSolver ( )

Successive calls to Solve will attempt to intelligently determine whether to re-initialise the internal CVODE solver, or whether we are simply extending the previous solution forward in time. This mechanism compares the state vector to its previous value, and the start time to the end of the last solve, which captures most cases where re-initialisation is required. However, changes to the RHS function can also require this, and cannot be automatically detected. In such cases users must call this function to force re-initialisation.

Definition at line 311 of file CvodeAdaptor.cpp.

References DeleteVector(), and mLastSolutionState.

Referenced by SetAutoReset().

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 101 of file CvodeAdaptor.hpp.

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

void CvodeAdaptor::SetAutoReset ( bool autoReset )

Set whether to automatically re-initialise CVODE on every call to Solve, or whether to attempt to guess when re-initialisation is needed. See also ResetSolver.

Parameters:

autoReset whether to reset on every Solve

Definition at line 292 of file CvodeAdaptor.cpp.

References mAutoReset, ResetSolver(), and SetMinimalReset().

Referenced by SetMinimalReset().

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 496 of file CvodeAdaptor.cpp.

References mMaxSteps.

void CvodeAdaptor::SetMinimalReset ( bool minimalReset )

Set whether to reduce the checking done when guessing when re-initialisation is needed, so it ignores changes in the state variables. If call with true argument, will call SetAutoReset(false).

Parameters:

minimalReset whether to avoid checking for changes in state variables

Definition at line 302 of file CvodeAdaptor.cpp.

References mForceMinimalReset, and SetAutoReset().

Referenced by SetAutoReset().

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 470 of file CvodeAdaptor.cpp.

References mAbsTol, 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

Initial conditions for the ODE solver.

Definition at line 181 of file CvodeAdaptor.cpp.

References DeleteVector(), EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), GetVectorSize(), mAbsTol, mAutoReset, mCheckForRoots, mData, mForceMinimalReset, mLastSolutionState, mLastSolutionTime, mMaxSteps, mpCvodeMem, mRelTol, CvodeData_::pSystem, CvodeData_::pY, and CompareDoubles::WithinAnyTolerance().

Referenced by Solve().

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 391 of file CvodeAdaptor.cpp.

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

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