AbstractCvodeSystem Class Reference

#include <AbstractCvodeSystem.hpp>

Inherits AbstractParameterisedSystem< N_Vector >.

Collaboration diagram for AbstractCvodeSystem:

Public Member Functions
	AbstractCvodeSystem (unsigned numberOfStateVariables)
virtual	~AbstractCvodeSystem ()
virtual void	EvaluateYDerivatives (realtype time, N_Vector y, N_Vector ydot)=0
void	SetAutoReset (bool autoReset)
void	ResetSolver ()
OdeSolution	Solve (realtype tStart, realtype tEnd, realtype maxDt, realtype tSamp)
void	Solve (realtype tStart, realtype tEnd, realtype maxDt)
void	SetMaxSteps (long int numSteps)
long int	GetMaxSteps ()
void	SetTolerances (double relTol=1e-5, double absTol=1e-7)
double	GetRelativeTolerance ()
double	GetAbsoluteTolerance ()
double	GetLastStepSize ()
Protected Member Functions
void	Init ()
Protected Attributes
bool	mUseAnalyticJacobian
double	mRelTol
double	mAbsTol
void *	mpCvodeMem
long int	mMaxSteps
double	mLastInternalStepSize
Private Member Functions
void	SetupCvode (N_Vector initialConditions, realtype tStart, realtype maxDt)
void	RecordStoppingPoint (double stopTime)
void	FreeCvodeMemory ()
void	CvodeError (int flag, const char *msg)
Private Attributes
N_Vector	mLastSolutionState
double	mLastSolutionTime
bool	mAutoReset

Detailed Description

Abstract OdeSystem class for Cvode systems (N_Vector instead of std::vector)

Sets up variables and functions for a general CVODE system.

ODE systems are specified primarily by the EvaluateYDerivatives() method, which calculates the right-hand side of the system.

Instances can store their state internally in the mStateVariables vector in our base class AbstractParameterisedSystem (see also GetNumberOfStateVariables(), SetStateVariables() and rGetStateVariables()), although this is not essential - the vector may be empty, in which case AbstractIvpOdeSolver::SolveAndUpdateStateVariable may not be used to solve the system.

CVODE systems may also have a vector of parameters, which can be accessed through the GetParameter() and SetParameter() methods of our base class.

Information about what the parameters and state variables represent is provided by a subclass of AbstractOdeSystemInformation. Various wrapper methods (e.g. rGetStateVariableNames()) are provided in our base class to access this information.

Also, subclasses may define a condition at which ODE solvers should stop prematurely. For this class CVODE solvers are being used, so CalculateRootFunction() should be used to detect the stopping time.

Definition at line 82 of file AbstractCvodeSystem.hpp.

Constructor & Destructor Documentation

AbstractCvodeSystem::AbstractCvodeSystem ( unsigned numberOfStateVariables )

Constructor.

Parameters:

numberOfStateVariables

the number of state variables in the ODE system

Definition at line 72 of file AbstractCvodeSystem.cpp.

References SetTolerances().

AbstractCvodeSystem::~AbstractCvodeSystem ( ) [virtual]

Virtual destructor since we have virtual methods.

Definition at line 96 of file AbstractCvodeSystem.cpp.

References DeleteVector(), FreeCvodeMemory(), mLastSolutionState, AbstractParameterisedSystem< N_Vector >::mParameters, and AbstractParameterisedSystem< N_Vector >::mStateVariables.

Member Function Documentation

void AbstractCvodeSystem::CvodeError	(	int	flag,
		const char *	msg
	)			`[private]`

Report an error from CVODE.

Parameters:

	flag	CVODE error code
	msg	Our description of the error

Definition at line 339 of file AbstractCvodeSystem.cpp.

References EXCEPTION.

Referenced by Solve().

virtual void AbstractCvodeSystem::EvaluateYDerivatives	(	realtype	time,
		N_Vector	y,
		N_Vector	ydot
	)			`[pure virtual]`

Method to evaluate the derivatives of the system.

Parameters:

	time	the current time
	y	the current values of the state variables
	ydot	storage for the derivatives of the system; will be filled in on return

void AbstractCvodeSystem::FreeCvodeMemory ( ) [private]

Free CVODE memory when finished with.

Definition at line 329 of file AbstractCvodeSystem.cpp.

References mpCvodeMem.

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

double AbstractCvodeSystem::GetAbsoluteTolerance ( )

Get the absolute tolerance.

Definition at line 219 of file AbstractCvodeSystem.cpp.

References mAbsTol.

double AbstractCvodeSystem::GetLastStepSize ( )

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

Definition at line 224 of file AbstractCvodeSystem.cpp.

References mLastInternalStepSize.

long int AbstractCvodeSystem::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 202 of file AbstractCvodeSystem.cpp.

References mMaxSteps.

double AbstractCvodeSystem::GetRelativeTolerance ( )

Get the relative tolerance.

Definition at line 214 of file AbstractCvodeSystem.cpp.

References mRelTol.

void AbstractCvodeSystem::Init ( ) [protected]

Must be called by concrete subclass constructors to initialise the state variables, after setting mpSystemInfo.

Definition at line 84 of file AbstractCvodeSystem.cpp.

References DeleteVector(), AbstractParameterisedSystem< N_Vector >::GetInitialConditions(), AbstractParameterisedSystem< N_Vector >::mParameters, AbstractParameterisedSystem< N_Vector >::mStateVariables, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().

void AbstractCvodeSystem::RecordStoppingPoint ( double stopTime ) [private]

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

Parameters:

stopTime

the finishing time

Definition at line 314 of file AbstractCvodeSystem.cpp.

References CreateVectorIfEmpty(), AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), mAutoReset, mLastSolutionState, mLastSolutionTime, AbstractParameterisedSystem< N_Vector >::mStateVariables, and SetVectorComponent().

Referenced by Solve().

void AbstractCvodeSystem::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 243 of file AbstractCvodeSystem.cpp.

References DeleteVector(), and mLastSolutionState.

Referenced by SetAutoReset(), SetTolerances(), and AbstractCvodeCell::SetVoltageDerivativeToZero().

void AbstractCvodeSystem::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 236 of file AbstractCvodeSystem.cpp.

References mAutoReset, and ResetSolver().

void AbstractCvodeSystem::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 (set by CVODE).

Parameters:

numSteps

new maximum

Definition at line 197 of file AbstractCvodeSystem.cpp.

References mMaxSteps.

void AbstractCvodeSystem::SetTolerances	(	double	relTol = `1e-5`,
		double	absTol = `1e-7`
	)

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 (defaults to 1e-5)
	absTol	the absolute tolerance for the solver (defaults to 1e-7)

Definition at line 207 of file AbstractCvodeSystem.cpp.

References mAbsTol, mRelTol, and ResetSolver().

Referenced by AbstractCvodeSystem().

void AbstractCvodeSystem::SetupCvode	(	N_Vector	initialConditions,
		realtype	tStart,
		realtype	maxDt
	)			`[private]`

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

Parameters:

	initialConditions	initial conditions
	tStart	start time of simulation
	maxDt	maximum time step to take

Definition at line 249 of file AbstractCvodeSystem.cpp.

References EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), mAbsTol, mAutoReset, mLastSolutionState, mLastSolutionTime, mMaxSteps, mpCvodeMem, mRelTol, and AbstractParameterisedSystem< N_Vector >::mStateVariables.

Referenced by Solve().

void AbstractCvodeSystem::Solve	(	realtype	tStart,
		realtype	tEnd,
		realtype	maxDt
	)

Simulate the cell, updating its internal state variables.

Uses the current values of the state variables at initial conditions. If the state variables have not been set (either by a prior solve, or a call to SetStateVariables) the initial conditions (given by GetInitialConditions) will be used.

Note:: See also the ResetSolver method.

Parameters:

	tStart	start time of simulation
	tEnd	end time of simulation
	maxDt	maximum time step to be taken by the adaptive solver (set this appropriately to avoid missing a stimulus)

Definition at line 170 of file AbstractCvodeSystem.cpp.

References CvodeError(), FreeCvodeMemory(), mLastInternalStepSize, mpCvodeMem, AbstractParameterisedSystem< N_Vector >::mStateVariables, RecordStoppingPoint(), SetupCvode(), and AbstractParameterisedSystem< N_Vector >::VerifyStateVariables().

OdeSolution AbstractCvodeSystem::Solve	(	realtype	tStart,
		realtype	tEnd,
		realtype	maxDt,
		realtype	tSamp
	)

Simulate the cell, returning a sampling of the state variables.

Uses the current values of the state variables at initial conditions. If the state variables have not been set (either by a prior solve, or a call to SetStateVariables) the initial conditions (given by GetInitialConditions) will be used.

The final values of the state variables will also be stored in this object.

Note:: See also the ResetSolver method.

Parameters:

	tStart	start time of simulation
	tEnd	end time of simulation
	maxDt	maximum time step to be taken by the adaptive solver (set this appropriately to avoid missing a stimulus)
	tSamp	sampling interval at which to store results