AbstractParameterisedSystem< VECTOR > Class Template Reference

#include <AbstractParameterisedSystem.hpp>

Inherits AbstractUntemplatedParameterisedSystem.

Collaboration diagram for AbstractParameterisedSystem< VECTOR >:

Public Member Functions
	AbstractParameterisedSystem (unsigned numberOfStateVariables)
VECTOR &	rGetStateVariables ()
VECTOR	GetStateVariables ()
void	SetStateVariables (const 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 VECTOR &rInitialConditions)
void	SetDefaultInitialCondition (unsigned index, double initialCondition)
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, VECTOR *pDerivedQuantities=NULL)
double	GetAnyVariable (const std::string &rName, double time=0.0, VECTOR *pDerivedQuantities=NULL)
void	SetAnyVariable (unsigned index, double value)
void	SetAnyVariable (const std::string &rName, double value)
virtual VECTOR	ComputeDerivedQuantities (double time, const VECTOR &rState)
VECTOR	ComputeDerivedQuantitiesFromCurrentState (double time)
Protected Member Functions
std::string	DumpState (const std::string &rMessage)
std::string	DumpState (const std::string &rMessage, VECTOR Y)
Protected Attributes
VECTOR	mStateVariables
VECTOR	mParameters
Private Member Functions
std::string	GetStateMessage (const std::string &message, VECTOR Y)
Friends
class	TestAbstractCvodeSystem

Detailed Description

template<typename VECTOR>
class AbstractParameterisedSystem< VECTOR >

This class contains the state variable and parameter vectors for an ODE system, along with methods to access these.

Its main purpose is to be a common base class for both AbstractOdeSystem and AbstractCvodeSystem, which require similar functionality but use different vector types.

Definition at line 303 of file AbstractParameterisedSystem.hpp.

Constructor & Destructor Documentation

template<typename VECTOR >

AbstractParameterisedSystem< VECTOR >::AbstractParameterisedSystem ( unsigned numberOfStateVariables ) [inline]

Constructor.

Parameters:

numberOfStateVariables

the number of state variables in the ODE system

Definition at line 45 of file AbstractParameterisedSystem.cpp.

References InitialiseEmptyVector(), AbstractParameterisedSystem< VECTOR >::mParameters, and AbstractParameterisedSystem< VECTOR >::mStateVariables.

Member Function Documentation

template<typename VECTOR>

VECTOR AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantities	(	double	time,
		const VECTOR &	rState
	)			`[inline, virtual]`

Compute the derived quantities from the given system state. Uses the current values for the parameters.

Parameters:

	time	the time at which to compute the derived quantities
	rState	values for the state variables

Definition at line 407 of file AbstractParameterisedSystem.cpp.

References EXCEPTION.

Referenced by AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantitiesFromCurrentState(), and OdeSolution::rGetDerivedQuantities().

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantitiesFromCurrentState ( double time ) [inline]

Compute the derived quantities based on the current system state.

Parameters:

time

the time at which to compute the derived quantities

Definition at line 414 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantities(), and AbstractParameterisedSystem< VECTOR >::mStateVariables.

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable().

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::DumpState	(	const std::string &	rMessage,
		VECTOR	Y
	)			`[inline, protected]`

Used to include extra debugging information in exception messages. For example, EXCEPTION(DumpState("Gating variable out of range", state_variables));

Parameters:

	rMessage	the exception message
	Y	the values of the state variables

Definition at line 77 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::GetStateMessage().

template<typename VECTOR >

std::string AbstractParameterisedSystem< VECTOR >::DumpState ( const std::string & rMessage ) [inline, protected]

Used to include extra debugging information in exception messages. For example, EXCEPTION(DumpState("Gating variable out of range"));

Parameters:

rMessage

the exception message

Definition at line 71 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::GetStateMessage(), and AbstractParameterisedSystem< VECTOR >::mStateVariables.

template<typename VECTOR>

double AbstractParameterisedSystem< VECTOR >::GetAnyVariable	(	const std::string &	rName,
		double	time = `0.0`,
		VECTOR *	pDerivedQuantities = `NULL`
	)			`[inline]`

Get the value of a variable, whether a state variable, parameter, or derived quantity.

Note that if the variable is a derived quantity, this method will compute all derived quantities, so may not be very efficient. To avoid this, pass a pre-computed vector of derived quantities as the optional third argument.

Parameters:

	rName	the name of the variable, (this method is the same as doing GetAnyVariableIndex(rName) and then calling the method above).
	time	the current simulation time, possibly needed if the variable is a derived quantity.
	pDerivedQuantities	optional vector of pre-computed derived quantity values.

Definition at line 345 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), and AbstractUntemplatedParameterisedSystem::GetAnyVariableIndex().

template<typename VECTOR>

double AbstractParameterisedSystem< VECTOR >::GetAnyVariable	(	unsigned	index,
		double	time = `0.0`,
		VECTOR *	pDerivedQuantities = `NULL`
	)			`[inline]`

Get the value of a variable, whether a state variable, parameter, or derived quantity.

Note that if the variable is a derived quantity, this method will compute all derived quantities, so may not be very efficient. To avoid this, pass a pre-computed vector of derived quantities as the optional third argument.

Parameters:

	index	the index of the variable, as given by GetAnyVariableIndex.
	time	the current simulation time, possibly needed if the variable is a derived quantity.
	pDerivedQuantities	optional vector of pre-computed derived quantity values.

Definition at line 308 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantitiesFromCurrentState(), DeleteVector(), EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfDerivedQuantities(), GetVectorComponent(), GetVectorSize(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< VECTOR >::mParameters, and AbstractParameterisedSystem< VECTOR >::mStateVariables.

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetInitialConditions ( ) const [inline]

Get the default initial conditions for this system.

Note:: Returns a fresh vector, which the caller should delete if appropriate for the type.

Definition at line 218 of file AbstractParameterisedSystem.cpp.

References CopyFromStdVector(), CreateVectorIfEmpty(), InitialiseEmptyVector(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, and AbstractUntemplatedParameterisedSystem::mpSystemInfo.

Referenced by WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), Alarcon2004OxygenBasedCellCycleModel::ResetForDivision(), and AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetParameter ( const std::string & rName ) const [inline]

Get the value of a given parameter.

Parameters:

rName

the name of the parameter

Definition at line 272 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::GetParameter(), and AbstractUntemplatedParameterisedSystem::GetParameterIndex().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetParameter ( unsigned index ) const [inline]

Get the value of a given parameter.

Parameters:

index

the index of the parameter

Definition at line 246 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorComponent(), GetVectorSize(), and AbstractParameterisedSystem< VECTOR >::mParameters.

Referenced by AbstractParameterisedSystem< VECTOR >::GetParameter(), OdeSolution::rGetParameters(), and HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::GetStateMessage	(	const std::string &	message,
		VECTOR	Y
	)			`[inline, private]`

Helper method to construct a string containing a dump of the vector

Parameters:

	message	a string to prefix (e.g. an error or the name of the vector)
	Y	a vector

Returns:: a string containing the contents of the vector.

Definition at line 84 of file AbstractParameterisedSystem.cpp.

References GetVectorComponent(), GetVectorSize(), and AbstractUntemplatedParameterisedSystem::rGetStateVariableNames().

Referenced by AbstractParameterisedSystem< VECTOR >::DumpState().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetStateVariable ( const std::string & rName ) const [inline]

Get the value of a given state variable.

Parameters:

rName

the name of the state variable

Definition at line 142 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::GetStateVariable(), and AbstractUntemplatedParameterisedSystem::GetStateVariableIndex().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetStateVariable ( unsigned index ) const [inline]

Get the value of a given state variable.

Parameters:

index

the index of the state variable

Definition at line 132 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorComponent(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, and AbstractParameterisedSystem< VECTOR >::mStateVariables.

Referenced by AbstractParameterisedSystem< VECTOR >::GetStateVariable().

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetStateVariables ( ) [inline]

Get a copy of the state variable vector. Caller takes responsibility for deleting the returned vector (if required for the VECTOR type).

Definition at line 112 of file AbstractParameterisedSystem.cpp.

References CopyVector(), and AbstractParameterisedSystem< VECTOR >::mStateVariables.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions ( ) [inline]

Reset the system's state variables to the default initial conditions.

Definition at line 229 of file AbstractParameterisedSystem.cpp.

References DeleteVector(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

template<typename VECTOR >

VECTOR & AbstractParameterisedSystem< VECTOR >::rGetStateVariables ( ) [inline]

Get the values of the state variables in the ODE system.

Definition at line 106 of file AbstractParameterisedSystem.cpp.

References AbstractParameterisedSystem< VECTOR >::mStateVariables.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetAnyVariable	(	const std::string &	rName,
		double	value
	)			`[inline]`

Set the value of a variable, whether a state variable or parameter. Attempting to set the value of a derived quantity will raise an exception.

Parameters:

	rName	the name of the variable.
	value	the value to give the variable.

Definition at line 381 of file AbstractParameterisedSystem.cpp.

References AbstractUntemplatedParameterisedSystem::GetAnyVariableIndex(), and AbstractParameterisedSystem< VECTOR >::SetAnyVariable().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetAnyVariable	(	unsigned	index,
		double	value
	)			`[inline]`

Set the value of a variable, whether a state variable or parameter. Attempting to set the value of a derived quantity will raise an exception.

Parameters:

	index	the index of the variable, as given by GetAnyVariableIndex.
	value	the value to give the variable.

Definition at line 364 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorSize(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< VECTOR >::mParameters, AbstractParameterisedSystem< VECTOR >::mStateVariables, and SetVectorComponent().

Referenced by AbstractParameterisedSystem< VECTOR >::SetAnyVariable().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetDefaultInitialCondition	(	unsigned	index,
		double	initialCondition
	)			`[inline]`

Set a single component of the default initial conditions for the system.

Note:: The default initial conditions are shared among all instances of the particular concrete system class.; This method DOES NOT change the state variables of the object on which it is called.

Parameters:

	index	the index of the state variable in the system
	initialCondition	the initial value for the state variable

Definition at line 207 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, and AbstractUntemplatedParameterisedSystem::mpSystemInfo.

template<typename VECTOR>

void AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions ( const VECTOR & rInitialConditions ) [inline]

Set the default initial conditions for the system.

Note:: The default initial conditions are shared among all instances of the particular concrete system class.; This method DOES NOT change the state variables of the object on which it is called.

Parameters:

rInitialConditions

vector containing initial values for the state variables

Definition at line 194 of file AbstractParameterisedSystem.cpp.

References CopyToStdVector(), EXCEPTION, GetVectorSize(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, and AbstractUntemplatedParameterisedSystem::mpSystemInfo.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetParameter	(	unsigned	index,
		double	value
	)			`[inline]`

Set the value of a given parameter.

Parameters:

	index	the index of the parameter
	value	the value

Definition at line 256 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorSize(), AbstractParameterisedSystem< VECTOR >::mParameters, and SetVectorComponent().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetParameter	(	const std::string &	rName,
		double	value
	)			`[inline]`

Set the value of a given parameter.

Parameters:

	rName	the name of the parameter
	value	the value

Definition at line 266 of file AbstractParameterisedSystem.cpp.

References AbstractUntemplatedParameterisedSystem::GetParameterIndex(), AbstractParameterisedSystem< VECTOR >::mParameters, and SetVectorComponent().

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetStateVariable	(	const std::string &	rName,
		double	newValue
	)			`[inline]`

Set the value of a single state variable in the ODE system.

Parameters:

	rName	name of the state variable to be set
	newValue	new value of the state variable

Definition at line 158 of file AbstractParameterisedSystem.cpp.

References AbstractUntemplatedParameterisedSystem::GetStateVariableIndex(), and AbstractParameterisedSystem< VECTOR >::SetStateVariable().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetStateVariable	(	unsigned	index,
		double	newValue
	)			`[inline]`

Set the value of a single state variable in the ODE system.

Parameters:

	index	index of the state variable to be set
	newValue	new value of the state variable

Definition at line 148 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< VECTOR >::mStateVariables, and SetVectorComponent().

Referenced by AdaptiveBidomainProblem::InitializeSolutionOnAdaptedMesh(), and AbstractParameterisedSystem< VECTOR >::SetStateVariable().

template<typename VECTOR>

void AbstractParameterisedSystem< VECTOR >::SetStateVariables ( const VECTOR & rStateVariables ) [inline]

Set the state variables equal to the values in the given vector, copying it. Caller thus maintains responsibility for deleting the input vector (if required for the VECTOR type).

Parameters:

rStateVariables

new values for the state variables

Definition at line 118 of file AbstractParameterisedSystem.cpp.

References CreateVectorIfEmpty(), EXCEPTION, GetVectorComponent(), GetVectorSize(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< VECTOR >::mStateVariables, and SetVectorComponent().

Referenced by WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), TysonNovakCellCycleModel::ResetForDivision(), AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), CellCycleModelOdeHandler::SetStateVariables(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems().

template<typename VECTOR>

virtual void AbstractParameterisedSystem< VECTOR >::VerifyStateVariables ( ) [inline, virtual]

Empty method which can be over-ridden and used in solvers to go through the current state vector and do range checking on the values (e.g. check that concentrations are positive and probabilities are between zero and one).

This method is overridden with a currently commented out method in AbstractCardiacCell which would be called by the ComputeExceptVoltage method (in heart).

This method is called by the AbstractCvodeSystem::Solve() method (in ode).

Reimplemented in CorriasBuistICCModified, and CorriasBuistSMCModified.

Definition at line 417 of file AbstractParameterisedSystem.hpp.