#include <AbstractCvodeSystem.hpp>

Inheritance diagram for AbstractCvodeSystem:

Collaboration diagram for AbstractCvodeSystem:

Public Member Functions
	AbstractCvodeSystem (unsigned numberOfStateVariables)

virtual	~AbstractCvodeSystem ()

virtual void	EvaluateYDerivatives (realtype time, const N_Vector y, N_Vector ydot)=0

virtual void	EvaluateAnalyticJacobian (long int N, realtype time, N_Vector y, N_Vector ydot, CHASTE_CVODE_DENSE_MATRIX jacobian, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3)

void	SetForceReset (bool autoReset)

void	SetMinimalReset (bool minimalReset)

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 ()

bool	GetUseAnalyticJacobian () const

bool	HasAnalyticJacobian () const

void	ForceUseOfNumericalJacobian (bool useNumericalJacobian=true)

Public Member Functions inherited from AbstractParameterisedSystem< N_Vector >
	AbstractParameterisedSystem (unsigned numberOfStateVariables)

N_Vector &	rGetStateVariables ()

N_Vector	GetStateVariables ()

void	SetStateVariables (const N_Vector &rStateVariables)

double	GetStateVariable (unsigned index) const

double	GetStateVariable (const std::string &rName) const

void	SetStateVariable (unsigned index, double newValue)

void	SetStateVariable (const std::string &rName, double newValue)

virtual void	VerifyStateVariables ()

void	SetDefaultInitialConditions (const N_Vector &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

N_Vector	GetInitialConditions () const

void	ResetToInitialConditions ()

double	GetParameter (unsigned index) const

double	GetParameter (const std::string &rName) const

void	SetParameter (const std::string &rName, double value)

void	SetParameter (unsigned index, double value)

double	GetAnyVariable (unsigned index, double time=0.0, N_Vector *pDerivedQuantities=NULL)

double	GetAnyVariable (const std::string &rName, double time=0.0, N_Vector *pDerivedQuantities=NULL)

void	SetAnyVariable (unsigned index, double value)

void	SetAnyVariable (const std::string &rName, double value)

virtual N_Vector	ComputeDerivedQuantities (double time, const N_Vector &rState)

N_Vector	ComputeDerivedQuantitiesFromCurrentState (double time)

Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
	AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)

virtual	~AbstractUntemplatedParameterisedSystem ()

boost::shared_ptr< const AbstractOdeSystemInformation >	GetSystemInformation () const

std::string	GetSystemName () const

unsigned	GetNumberOfAttributes () const

bool	HasAttribute (const std::string &rName) const

double	GetAttribute (const std::string &rName) const

unsigned	GetNumberOfStateVariables () const

const std::vector< std::string > &	rGetStateVariableNames () const

const std::vector< std::string > &	rGetStateVariableUnits () const

unsigned	GetStateVariableIndex (const std::string &rName) const

bool	HasStateVariable (const std::string &rName) const

std::string	GetStateVariableUnits (unsigned index) const

unsigned	GetNumberOfParameters () const

const std::vector< std::string > &	rGetParameterNames () const

const std::vector< std::string > &	rGetParameterUnits () const

unsigned	GetParameterIndex (const std::string &rName) const

bool	HasParameter (const std::string &rName) const

std::string	GetParameterUnits (unsigned index) const

unsigned	GetNumberOfDerivedQuantities () const

const std::vector< std::string > &	rGetDerivedQuantityNames () const

const std::vector< std::string > &	rGetDerivedQuantityUnits () const

unsigned	GetDerivedQuantityIndex (const std::string &rName) const

bool	HasDerivedQuantity (const std::string &rName) const

std::string	GetDerivedQuantityUnits (unsigned index) const

unsigned	GetAnyVariableIndex (const std::string &rName) const

bool	HasAnyVariable (const std::string &rName) const

std::string	GetAnyVariableUnits (unsigned index) const

std::string	GetAnyVariableUnits (const std::string &rName) const

Protected Member Functions
void	Init ()

Protected Member Functions inherited from AbstractParameterisedSystem< N_Vector >
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, N_VectorY)

std::string	DumpState (const std::string &rMessage, N_VectorY, double time)

void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)

Protected Attributes
bool	mHasAnalyticJacobian

bool	mUseAnalyticJacobian

double	mRelTol

double	mAbsTol

void *	mpCvodeMem

long int	mMaxSteps

double	mLastInternalStepSize

Protected Attributes inherited from AbstractParameterisedSystem< N_Vector >
N_Vector	mStateVariables

N_Vector	mParameters

Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned	mNumberOfStateVariables

boost::shared_ptr< AbstractOdeSystemInformation >	mpSystemInfo

Private Member Functions
template<class Archive >
void	save (Archive &archive, const unsigned int version) const

template<class Archive >
void	load (Archive &archive, const unsigned int version)

void	SetupCvode (N_Vector initialConditions, realtype tStart, realtype maxDt)

void	RecordStoppingPoint (double stopTime)

void	FreeCvodeMemory ()

void	CvodeError (int flag, const char *msg, const double &rTime, const double &rStartTime, const double &rEndTime)

Private Attributes
N_Vector	mLastSolutionState

double	mLastSolutionTime

bool	mForceReset

bool	mForceMinimalReset

Friends
class	TestAbstractCvodeSystem

class	boost::serialization::access

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.

You can also specify an EvaluateAnalyticJacobian() method which will allow CVODE to evaluate the Jacobian matrix precisely instead of using multiple calls to EvaluateYDerivatives() to make an approximation to it. This generally provides extra accuracy and better convergence, and so gives a speed up for a given tolerance. Cardiac action potential model Jacobians are calculated automatically by PyCML (see python/pycml) via Maple for symbolic differentiation.

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.

Note that the default tolerances for the solver are set by SetTolerances(), these can make quite a difference to the time it takes to solve the ODE system.

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 - 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 119 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 141 of file AbstractCvodeSystem.cpp.

References SetTolerances().

AbstractCvodeSystem::~AbstractCvodeSystem ( )

virtual

Virtual destructor since we have virtual methods.

Definition at line 174 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,
		const double &	rTime,
		const double &	rStartTime,
		const double &	rEndTime
	)

private

Report an error from CVODE.

Parameters

flag	CVODE error code
msg	Our description of the error
rTime	The time that the solver got to
rStartTime	The time that the solver started at.
rEndTime	The time that the solver was supposed to solve up to.

Definition at line 469 of file AbstractCvodeSystem.cpp.

References EXCEPTION, FreeCvodeMemory(), MakeStdVec(), mpCvodeMem, AbstractParameterisedSystem< N_Vector >::mStateVariables, and AbstractUntemplatedParameterisedSystem::rGetStateVariableNames().

Referenced by load(), and Solve().

virtual void AbstractCvodeSystem::EvaluateAnalyticJacobian	(	long int	N,
		realtype	time,
		N_Vector	y,
		N_Vector	ydot,
		CHASTE_CVODE_DENSE_MATRIX	jacobian,
		N_Vector	tmp1,
		N_Vector	tmp2,
		N_Vector	tmp3
	)

inlinevirtual

This method is called by AbstractCvodeSystemJacAdaptor method in the .cpp file.

It provides an interface between the methods different versions of CVODE are expecting and the Jacobians provided by Chaste CVODE systems.

Parameters

N	the size of the ODE system
time	the current time (used by ODE systems like y' = f(t,y) only I guess)
y	the current state variables y for y' = f(t,y)
ydot	the current set of derivatives y' = f(t,y)
jacobian	a pointer to a jacobian, populated by this method.
tmp1	working memory of the correct size provided by CVODE for temporary calculations
tmp2	working memory of the correct size provided by CVODE for temporary calculations
tmp3	working memory of the correct size provided by CVODE for temporary calculations

Definition at line 331 of file AbstractCvodeSystem.hpp.

References CLASS_IS_ABSTRACT, EXCEPTION, ForceUseOfNumericalJacobian(), GetAbsoluteTolerance(), GetLastStepSize(), GetMaxSteps(), GetRelativeTolerance(), GetUseAnalyticJacobian(), HasAnalyticJacobian(), ResetSolver(), SetForceReset(), SetMaxSteps(), SetMinimalReset(), SetTolerances(), and Solve().

virtual void AbstractCvodeSystem::EvaluateYDerivatives	(	realtype	time,
		const 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::ForceUseOfNumericalJacobian ( bool useNumericalJacobian = true )

Force the use of a numerical Jacobian, even if an analytic form is provided. This is needed for a handful of troublesome models.

Parameters

useNumericalJacobian Whether to use a numerical instead of the analytic Jacobian.

Definition at line 520 of file AbstractCvodeSystem.cpp.

References EXCEPTION, FreeCvodeMemory(), mHasAnalyticJacobian, and mUseAnalyticJacobian.

Referenced by EvaluateAnalyticJacobian().

void AbstractCvodeSystem::FreeCvodeMemory ( )

private

Free CVODE memory when finished with.

Definition at line 459 of file AbstractCvodeSystem.cpp.

References mpCvodeMem.

Referenced by CvodeError(), ForceUseOfNumericalJacobian(), load(), and ~AbstractCvodeSystem().

double AbstractCvodeSystem::GetAbsoluteTolerance ( )

Returns: the absolute tolerance.

Definition at line 324 of file AbstractCvodeSystem.cpp.

References mAbsTol.

Referenced by EvaluateAnalyticJacobian().

double AbstractCvodeSystem::GetLastStepSize ( )

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

Definition at line 329 of file AbstractCvodeSystem.cpp.

References mLastInternalStepSize.

Referenced by EvaluateAnalyticJacobian().

long int AbstractCvodeSystem::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 307 of file AbstractCvodeSystem.cpp.

References mMaxSteps.

Referenced by EvaluateAnalyticJacobian().

double AbstractCvodeSystem::GetRelativeTolerance ( )

Returns: the relative tolerance.

Definition at line 319 of file AbstractCvodeSystem.cpp.

References mRelTol.

Referenced by EvaluateAnalyticJacobian().

bool AbstractCvodeSystem::GetUseAnalyticJacobian ( ) const

Returns: whether an analytic Jacobian is used (mUseAnalyticJacobian).

Definition at line 514 of file AbstractCvodeSystem.cpp.

References mUseAnalyticJacobian.

Referenced by EvaluateAnalyticJacobian().

bool AbstractCvodeSystem::HasAnalyticJacobian ( ) const

Returns: whether the ODE system has an analytic Jacobian (mHasAnalyticJacobian).

Definition at line 509 of file AbstractCvodeSystem.cpp.

References mHasAnalyticJacobian.

Referenced by EvaluateAnalyticJacobian().

void AbstractCvodeSystem::Init ( )

protected

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

Definition at line 162 of file AbstractCvodeSystem.cpp.

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

template<class Archive >

void AbstractCvodeSystem::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 175 of file AbstractCvodeSystem.hpp.

References AbstractParameterisedSystem< N_Vector >::CheckParametersOnLoad(), CopyFromStdVector(), CvodeError(), FreeCvodeMemory(), mAbsTol, mForceMinimalReset, mForceReset, mHasAnalyticJacobian, mLastInternalStepSize, mLastSolutionTime, mMaxSteps, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, mUseAnalyticJacobian, RecordStoppingPoint(), and SetupCvode().

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 438 of file AbstractCvodeSystem.cpp.

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

Referenced by load(), and 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 353 of file AbstractCvodeSystem.cpp.

References DeleteVector(), and mLastSolutionState.

Referenced by EvaluateAnalyticJacobian(), SetForceReset(), SetTolerances(), and AbstractCvodeCell::SetVoltageDerivativeToZero().

template<class Archive >

void AbstractCvodeSystem::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Archive the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 132 of file AbstractCvodeSystem.hpp.

References mAbsTol, MakeStdVec(), mForceMinimalReset, mForceReset, mHasAnalyticJacobian, mLastInternalStepSize, mLastSolutionTime, mMaxSteps, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< N_Vector >::mParameters, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, mUseAnalyticJacobian, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().

void AbstractCvodeSystem::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. For example it will re-initialise if the time changes, or any state variables change. You can safely change parameters between solve calls with or without resets.

See also ResetSolver and SetMinimalReset

Parameters

autoReset whether to reset on every Solve

Definition at line 334 of file AbstractCvodeSystem.cpp.

References mForceReset, and ResetSolver().

Referenced by EvaluateAnalyticJacobian(), and SetMinimalReset().

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 302 of file AbstractCvodeSystem.cpp.

References mMaxSteps.

Referenced by EvaluateAnalyticJacobian().

void AbstractCvodeSystem::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 called with true argument, will call SetForceReset(false). You can safely change parameters between solve calls with or without resets.

Parameters

minimalReset whether to avoid checking for changes in state variables

Definition at line 343 of file AbstractCvodeSystem.cpp.

References mForceMinimalReset, and SetForceReset().

Referenced by EvaluateAnalyticJacobian().

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 312 of file AbstractCvodeSystem.cpp.

References mAbsTol, mRelTol, and ResetSolver().

Referenced by AbstractCvodeSystem(), and EvaluateAnalyticJacobian().

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 359 of file AbstractCvodeSystem.cpp.

References EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), mAbsTol, mForceMinimalReset, mForceReset, mLastSolutionState, mLastSolutionTime, mMaxSteps, mpCvodeMem, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, mUseAnalyticJacobian, and CompareDoubles::WithinAnyTolerance().

Referenced by load(), and Solve().

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

Returns: the solution object with results at each sampling step

Definition at line 189 of file AbstractCvodeSystem.cpp.

References TimeStepper::AdvanceOneTimeStep(), CvodeError(), TimeStepper::EstimateTimeSteps(), TimeStepper::GetNextTime(), TimeStepper::GetTime(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), MakeStdVec(), mLastInternalStepSize, mpCvodeMem, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< N_Vector >::mStateVariables, RecordStoppingPoint(), OdeSolution::rGetSolutions(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), SetupCvode(), UNUSED_OPT, and AbstractParameterisedSystem< N_Vector >::VerifyStateVariables().

Referenced by AbstractCvodeCell::Compute(), EvaluateAnalyticJacobian(), and AbstractCvodeCell::SolveAndUpdateState().

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 249 of file AbstractCvodeSystem.cpp.

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