#include <AbstractOdeSystem.hpp>

Inheritance diagram for AbstractOdeSystem:

Collaboration diagram for AbstractOdeSystem:

Public Member Functions
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

virtual void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)=0

virtual bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)

virtual double	CalculateRootFunction (double time, const std::vector< double > &rY)

bool	GetUseAnalyticJacobian ()

const std::vector< double > &	rGetConstStateVariables () const

Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
	AbstractParameterisedSystem (unsigned numberOfStateVariables)

std::vector< double > &	rGetStateVariables ()

std::vector< double >	GetStateVariables ()

void	SetStateVariables (const std::vector< double > &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 std::vector< double > &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

std::vector< double >	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, std::vector< double > *pDerivedQuantities=NULL)

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

void	SetAnyVariable (unsigned index, double value)

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

virtual std::vector< double >	ComputeDerivedQuantities (double time, const std::vector< double > &rState)

std::vector< double >	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 Attributes
bool	mUseAnalyticJacobian

Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< double >	mStateVariables

std::vector< double >	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)

Friends
class	TestAbstractOdeSystem

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y, double time)

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

Detailed Description

Abstract OdeSystem class.

Sets up variables and functions for a general ODE 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.

ODE 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.

There are two more advanced facilities available for subclass authors. An analytic form for the Jacobian matrix of the system may be provided, in which case you must subclass AbstractOdeSystemWithAnalyticJacobian. The GetUseAnalyticJacobian() method will test whether this is the case.

Also, subclasses may define a condition at which ODE solvers should stop prematurely. For the Chaste solvers this is done by overriding CalculateStoppingEvent(); if the more advanced CVODE solvers are being used then implement CalculateRootFunction() instead to detect the stopping time more accurately.

Definition at line 87 of file AbstractOdeSystem.hpp.

Constructor & Destructor Documentation

AbstractOdeSystem::AbstractOdeSystem ( unsigned numberOfStateVariables )

Constructor.

Parameters

numberOfStateVariables the number of state variables in the ODE system

Definition at line 39 of file AbstractOdeSystem.cpp.

AbstractOdeSystem::~AbstractOdeSystem ( )

virtual

Virtual destructor since we have virtual methods.

Definition at line 45 of file AbstractOdeSystem.cpp.

Member Function Documentation

double AbstractOdeSystem::CalculateRootFunction	(	double	time,
		const std::vector< double > &	rY
	)

virtual

An alternative approach to stopping events; currently only useful with CVODE. CVODE can search for roots (zeros) of this function while solving the ODE system, and home in on them to find sign transitions to high precision.

The default implementation here fakes a root function using CalculateStoppingEvent.

Parameters

time	the current time
rY	the current values of the state variables

Returns: value of the root function

Reimplemented in VanLeeuwen2009WntSwatCellCycleOdeSystem, WntCellCycleOdeSystem, and TysonNovak2001OdeSystem.

Definition at line 54 of file AbstractOdeSystem.cpp.

References CalculateStoppingEvent().

bool AbstractOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)

virtual

CalculateStoppingEvent() - can be overloaded if the ODE is to be solved only until a particular event (for example, only until the y value becomes negative.

After each timestep the solver will call this method on the ODE to see if it should stop there.

Returns: true if the solver should stop now. By default, false is returned here.

Parameters

time	the current time
rY	the current values of the state variables

Reimplemented in VanLeeuwen2009WntSwatCellCycleOdeSystem, WntCellCycleOdeSystem, TysonNovak2001OdeSystem, and Alarcon2004OxygenBasedCellCycleOdeSystem.

Definition at line 49 of file AbstractOdeSystem.cpp.

Referenced by CalculateRootFunction(), AbstractOneStepIvpOdeSolver::InternalSolve(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), AbstractOneStepIvpOdeSolver::Solve(), RungeKuttaFehlbergIvpOdeSolver::Solve(), and CvodeAdaptor::Solve().

virtual void AbstractOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)

pure virtual

Method to evaluate the derivatives of the system.

Parameters

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

Implemented in AbstractBackwardEulerCardiacCell< 0u >, VanLeeuwen2009WntSwatCellCycleOdeSystem, CorriasBuistICCModified, NhsContractionModel, WntCellCycleOdeSystem, TysonNovak2001OdeSystem, CorriasBuistSMCModified, AbstractBackwardEulerCardiacCell< SIZE >, AbstractGeneralizedRushLarsenCardiacCell, Alarcon2004OxygenBasedCellCycleOdeSystem, Mirams2010WntOdeSystem, AbstractRushLarsenCardiacCell, CombinedOdeSystem, Kerchoffs2003ContractionModel, CML_noble_varghese_kohl_noble_1998_basic_with_sac, DeltaNotchOdeSystem, FakeBathCell, Goldbeter1991OdeSystem, Nash2004ContractionModel, OdeSystemForCoupledHeatEquation, OdeSystemForCoupledHeatEquationWithSource, and FitzHughNagumo1961OdeSystem.

Referenced by HeunIvpOdeSolver::CalculateNextYValue(), RungeKutta2IvpOdeSolver::CalculateNextYValue(), RungeKutta4IvpOdeSolver::CalculateNextYValue(), EulerIvpOdeSolver::CalculateNextYValue(), GRL1IvpOdeSolver::CalculateNextYValue(), GRL2IvpOdeSolver::CalculateNextYValue(), RungeKuttaFehlbergIvpOdeSolver::CalculateNextYValue(), and BackwardEulerIvpOdeSolver::ComputeResidual().

bool AbstractOdeSystem::GetUseAnalyticJacobian ( )

Get whether an analytic Jacobian is used.

Returns: mUseAnalyticJacobian

Definition at line 60 of file AbstractOdeSystem.cpp.

References mUseAnalyticJacobian.

Referenced by BackwardEulerIvpOdeSolver::ComputeJacobian().

template<class Archive >

void AbstractOdeSystem::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 129 of file AbstractOdeSystem.hpp.

References AbstractParameterisedSystem< std::vector< double > >::CheckParametersOnLoad(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractParameterisedSystem< std::vector< double > >::mStateVariables, and mUseAnalyticJacobian.

const std::vector< double > & AbstractOdeSystem::rGetConstStateVariables ( ) const

Todo:: move to AbstractParameterisedSystem? (1540)

Returns: const reference to the state variables in the ODE system (used in archiving).

Definition at line 65 of file AbstractOdeSystem.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mStateVariables.

template<class Archive >

void AbstractOdeSystem::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 102 of file AbstractOdeSystem.hpp.

References AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractParameterisedSystem< std::vector< double > >::mStateVariables, mUseAnalyticJacobian, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().

Member Data Documentation

bool AbstractOdeSystem::mUseAnalyticJacobian

protected

Whether to use an analytic Jacobian.

Definition at line 154 of file AbstractOdeSystem.hpp.

Referenced by AbstractOdeSystemWithAnalyticJacobian::AbstractOdeSystemWithAnalyticJacobian(), AbstractGeneralizedRushLarsenCardiacCell::ForceUseOfNumericalJacobian(), GetUseAnalyticJacobian(), load(), and save().

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

ode/src/common/AbstractOdeSystem.hpp
ode/src/common/AbstractOdeSystem.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation