#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	SetForceReset (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 ()

Public Member Functions inherited from AbstractIvpOdeSolver
virtual void	SolveAndUpdateStateVariable (AbstractOdeSystem *pAbstractOdeSystem, double startTime, double endTime, double timeStep)

bool	StoppingEventOccurred ()

double	GetStoppingTime ()

	AbstractIvpOdeSolver ()

virtual	~AbstractIvpOdeSolver ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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	mForceReset

bool	mForceMinimalReset

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractIvpOdeSolver
bool	mStoppingEventOccurred

double	mStoppingTime

Detailed Description

The CVODE adaptor ODE solver class. This class is used as a solver for Chaste standard AbstractOdeSystems that have a native vector type of std::vector<double> and so can be used to apply CVODE to systems that could also be solved with the other solvers in this folder.

N.B. If you know you are always going to want to use CVODE to solve your system, then it will be faster to write your system so it uses N_Vectors natively as an AbstractCvodeSystem. AbstractCvodeSystems have an in-built CVODE solver, and therefore don't need to use this class. For Chaste developers - this means there is some duplication of code between this class and AbstractCvodeSystem as both set up and use CVODE to solve systems. If you change one you should probably change both!

This 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.

Repeated calls to Solve will no longer set up and delete CVODE memory, unless the following method is called:

SetForceReset(true) - reset each time Solve() is called

default behaviour - reset if state variables change, or we ask to solve from a different time than the last solve call finished.

SetMinimalReset(true) - ignore changes in state vars and just reset if the time is inconsistent.

Definition at line 105 of file CvodeAdaptor.hpp.

Constructor & Destructor Documentation

◆ CvodeAdaptor()

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 564 of file CvodeAdaptor.cpp.

◆ ~CvodeAdaptor()

CvodeAdaptor::~CvodeAdaptor ( )

Destructor. Frees memory.

Definition at line 588 of file CvodeAdaptor.cpp.

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

Member Function Documentation

◆ CheckForStoppingEvents()

void CvodeAdaptor::CheckForStoppingEvents ( )

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

By default we do not check.

Definition at line 629 of file CvodeAdaptor.cpp.

References mCheckForRoots.

◆ CvodeError()

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 425 of file CvodeAdaptor.cpp.

References EXCEPTION.

Referenced by Solve(), and Solve().

◆ FreeCvodeMemory()

void CvodeAdaptor::FreeCvodeMemory ( )

protected

Free CVODE memory after solving a system of ODEs.

Definition at line 375 of file CvodeAdaptor.cpp.

References mpCvodeMem.

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

◆ GetAbsoluteTolerance()

double CvodeAdaptor::GetAbsoluteTolerance ( )

Returns: the absolute tolerance.

Definition at line 619 of file CvodeAdaptor.cpp.

References mAbsTol.

◆ GetLastStepSize()

double CvodeAdaptor::GetLastStepSize ( )

Returns: the last step size used internally by CVODE in the last Solve call

Definition at line 624 of file CvodeAdaptor.cpp.

References mLastInternalStepSize.

◆ GetMaxSteps()

long int CvodeAdaptor::GetMaxSteps ( )

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

Definition at line 639 of file CvodeAdaptor.cpp.

References mMaxSteps.

◆ GetRelativeTolerance()

double CvodeAdaptor::GetRelativeTolerance ( )

Returns: the relative tolerance.

Definition at line 614 of file CvodeAdaptor.cpp.

References mRelTol.

◆ RecordStoppingPoint()

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 594 of file CvodeAdaptor.cpp.

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

Referenced by Solve(), and Solve().

◆ ResetSolver()

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 419 of file CvodeAdaptor.cpp.

References DeleteVector(), and mLastSolutionState.

Referenced by SetForceReset().

◆ serialize()

template<class Archive >

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

inlineprivate

Archive, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 117 of file CvodeAdaptor.hpp.

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

◆ SetForceReset()

void CvodeAdaptor::SetForceReset ( 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 400 of file CvodeAdaptor.cpp.

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

Referenced by SetMinimalReset().

◆ SetMaxSteps()

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 634 of file CvodeAdaptor.cpp.

References mMaxSteps.

◆ SetMinimalReset()

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 SetForceReset(false).

Parameters

minimalReset whether to avoid checking for changes in state variables

Definition at line 410 of file CvodeAdaptor.cpp.

References mForceMinimalReset, and SetForceReset().

Referenced by SetForceReset().

◆ SetTolerances()

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 608 of file CvodeAdaptor.cpp.

References mAbsTol, and mRelTol.

◆ SetupCvode()

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 191 of file CvodeAdaptor.cpp.

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

Referenced by Solve(), and Solve().

◆ Solve() [1/2]

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 509 of file CvodeAdaptor.cpp.

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

◆ Solve() [2/2]

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 436 of file CvodeAdaptor.cpp.

References TimeStepper::AdvanceOneTimeStep(), AbstractOdeSystem::CalculateStoppingEvent(), CvodeError(), DeleteVector(), TimeStepper::EstimateTimeSteps(), EXCEPTION, FreeCvodeMemory(), TimeStepper::GetNextTime(), AbstractUntemplatedParameterisedSystem::GetSystemInformation(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), mCheckForRoots, mLastInternalStepSize, mLastSolutionTime, mpCvodeMem, AbstractIvpOdeSolver::mStoppingEventOccurred, AbstractIvpOdeSolver::mStoppingTime, RecordStoppingPoint(), OdeSolution::rGetSolutions(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), SetupCvode(), and UNUSED_OPT.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 109 of file CvodeAdaptor.hpp.

Member Data Documentation

◆ mAbsTol

double CvodeAdaptor::mAbsTol

private

Absolute tolerance for the ODE solver.

Definition at line 138 of file CvodeAdaptor.hpp.

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

◆ mCheckForRoots

bool CvodeAdaptor::mCheckForRoots

private

Whether to check for stopping events.

Definition at line 150 of file CvodeAdaptor.hpp.

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

◆ mData

CvodeData CvodeAdaptor::mData

private

The CVODE data structure.

Definition at line 132 of file CvodeAdaptor.hpp.

Referenced by SetupCvode().

◆ mForceMinimalReset

bool CvodeAdaptor::mForceMinimalReset

private

Whether to ignore changes in the state variables when deciding whether to reset.

Definition at line 162 of file CvodeAdaptor.hpp.

Referenced by SetMinimalReset(), and SetupCvode().

◆ mForceReset

bool CvodeAdaptor::mForceReset

private

Whether to automatically reset CVODE on each Solve call.

Definition at line 159 of file CvodeAdaptor.hpp.

Referenced by RecordStoppingPoint(), SetForceReset(), and SetupCvode().

◆ mLastInternalStepSize

double CvodeAdaptor::mLastInternalStepSize

private

The size of the previous timestep.

Definition at line 141 of file CvodeAdaptor.hpp.

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

◆ mLastSolutionState

N_Vector CvodeAdaptor::mLastSolutionState

private

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

Definition at line 153 of file CvodeAdaptor.hpp.

Referenced by ~CvodeAdaptor(), RecordStoppingPoint(), ResetSolver(), and SetupCvode().

◆ mLastSolutionTime

double CvodeAdaptor::mLastSolutionTime

private

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

Definition at line 156 of file CvodeAdaptor.hpp.

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

◆ mMaxSteps

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 147 of file CvodeAdaptor.hpp.

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

◆ mpCvodeMem

void* CvodeAdaptor::mpCvodeMem

private

Pointer to the CVODE memory block.

Definition at line 129 of file CvodeAdaptor.hpp.

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

◆ mRelTol

double CvodeAdaptor::mRelTol

private

Relative tolerance for the ODE solver.

Definition at line 135 of file CvodeAdaptor.hpp.

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

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

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CvodeAdaptor()

◆ ~CvodeAdaptor()

Member Function Documentation

◆ CheckForStoppingEvents()

◆ CvodeError()

◆ FreeCvodeMemory()

◆ GetAbsoluteTolerance()

◆ GetLastStepSize()

◆ GetMaxSteps()

◆ GetRelativeTolerance()

◆ RecordStoppingPoint()

◆ ResetSolver()

◆ serialize()

◆ SetForceReset()

◆ SetMaxSteps()

◆ SetMinimalReset()

◆ SetTolerances()

◆ SetupCvode()

◆ Solve() [1/2]

◆ Solve() [2/2]

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mAbsTol

◆ mCheckForRoots

◆ mData

◆ mForceMinimalReset

◆ mForceReset

◆ mLastInternalStepSize

◆ mLastSolutionState

◆ mLastSolutionTime

◆ mMaxSteps

◆ mpCvodeMem

◆ mRelTol