#include <AbstractOdeSystemInformation.hpp>

Inheritance diagram for AbstractOdeSystemInformation:

Collaboration diagram for AbstractOdeSystemInformation:

Public Member Functions
	AbstractOdeSystemInformation ()
virtual	~AbstractOdeSystemInformation ()
std::string	GetSystemName () const
std::string	GetFreeVariableName () const
std::string	GetFreeVariableUnits () const
void	SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)
void	SetDefaultInitialCondition (unsigned index, double initialCondition)
std::vector< double >	GetInitialConditions () 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
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	GetNumberOfParameters () const
unsigned	GetAnyVariableIndex (const std::string &rName) const
bool	HasAnyVariable (const std::string &rName) const
std::string	GetAnyVariableUnits (unsigned index) 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	GetNumberOfDerivedQuantities () const
unsigned	GetNumberOfAttributes () const
bool	HasAttribute (const std::string &rName) const
double	GetAttribute (const std::string &rName) const
Protected Member Functions
virtual void	Initialise ()=0
Protected Attributes
std::string	mSystemName
std::string	mFreeVariableName
std::string	mFreeVariableUnits
std::vector< std::string >	mVariableNames
std::vector< std::string >	mVariableUnits
std::vector< std::string >	mParameterNames
std::vector< std::string >	mParameterUnits
std::vector< std::string >	mDerivedQuantityNames
std::vector< std::string >	mDerivedQuantityUnits
std::map< std::string, double >	mAttributes
std::vector< double >	mInitialConditions
bool	mInitialised
Friends
class	TestAbstractOdeSystem

Detailed Description

An abstract class which provides access to information about a particular ODE system *class* (as opposed to an instance).

The information available includes:

a name for the system
name & units of the free variable
names & units of state variables
suggested initial conditions
names & units of (settable) parameters
names & units of derived quantities

This class requires a subclass defining the Initialise method in order to set up the information. Developers may do this by defining their own subclass, but the most convenient method is likely to be to use the OdeSystemInformation class, which is a templated singleton subclass of this AbstractOdeSystemInformation class. See its documentation for details of how to use it.

Definition at line 62 of file AbstractOdeSystemInformation.hpp.

Constructor & Destructor Documentation

AbstractOdeSystemInformation::AbstractOdeSystemInformation ( )

Constructor.

Definition at line 43 of file AbstractOdeSystemInformation.cpp.

AbstractOdeSystemInformation::~AbstractOdeSystemInformation ( ) [virtual]

Virtual destructor since we have virtual methods.

Definition at line 48 of file AbstractOdeSystemInformation.cpp.

Member Function Documentation

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

Get the index of a variable, whether a state variable, parameter, or derived quantity, with the given name. The returned index is suitable for use with GetAnyVariableUnits.

Indices go through Variables, Parameters then derived quantities.

Parameters:

rName the name of a variable

Definition at line 171 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, GetDerivedQuantityIndex(), GetParameterIndex(), GetStateVariableIndex(), HasDerivedQuantity(), HasParameter(), HasStateVariable(), mInitialised, mParameterNames, and mVariableNames.

std::string AbstractOdeSystemInformation::GetAnyVariableUnits ( unsigned index ) const

Get the units of a variable, whether a state variable, parameter, or derived quantity, given its index as returned by GetAnyVariableIndex.

Parameters:

index an index from GetAnyVariableIndex.

Returns:: the units of the variable.

Definition at line 199 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityUnits, mInitialised, mParameterUnits, and mVariableUnits.

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

Get the value of a named attribute.

Parameters:

rName the attribute name.

Definition at line 287 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mAttributes, and mInitialised.

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

Get the index of a derived quantity, given its name.

Parameters:

rName the name of a derived quantity.

Definition at line 241 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityNames, and mInitialised.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::GetDerivedQuantityUnits ( unsigned index ) const

Get the units of a derived quantity.

Parameters:

index an index from GetDerivedQuantityIndex.

Returns:: the units of the variable.

Definition at line 259 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityUnits, and mInitialised.

std::string AbstractOdeSystemInformation::GetFreeVariableName ( ) const

Get the name of the free variable in this system of ODEs.

Definition at line 57 of file AbstractOdeSystemInformation.cpp.

References mFreeVariableName.

std::string AbstractOdeSystemInformation::GetFreeVariableUnits ( ) const

Get the units of the free variable in this system of ODEs.

Definition at line 62 of file AbstractOdeSystemInformation.cpp.

References mFreeVariableUnits.

std::vector< double > AbstractOdeSystemInformation::GetInitialConditions ( ) const

Get a copy of the suggested initial conditions.

Definition at line 79 of file AbstractOdeSystemInformation.cpp.

References mInitialConditions, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfAttributes ( ) const

Returns:: the number of named attributes that this system has.

Definition at line 275 of file AbstractOdeSystemInformation.cpp.

References mAttributes, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfDerivedQuantities ( ) const

Returns:: the number of derived quantities in this system

Definition at line 269 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityUnits, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfParameters ( ) const

Returns:: The number of parameters in this parameterised system.

Definition at line 165 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterUnits.

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

This method is used to establish a parameter's position within the vector of parameters of an ODE system. This number can then be used with the method GetParameterUnits.

Parameters:

rName the name of a parameter

Returns:: the parameter's position within the vector of parameters associated with the ODE system.

Definition at line 137 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mParameterNames.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::GetParameterUnits ( unsigned index ) const

Get the units of a parameter given its index in the ODE system.

Parameters:

index a state variable's position within the vector of state variables associated with the ODE system.

Returns:: the units of the state variable.

Definition at line 155 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mParameterUnits.

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

This method is used to establish a state varible's position within the vector of state variables of an ODE system. This number can then be used with the method GetStateVariableUnits.

Parameters:

rName the name of a state variable

Returns:: the state variable's position within the vector of state variables associated with the ODE system.

Definition at line 97 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mVariableNames.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::GetStateVariableUnits ( unsigned index ) const

Get the units of a state variable given its index in the ODE system.

Parameters:

index a state variable's position within the vector of state variables associated with the ODE system.

Returns:: the units of the state variable.

Definition at line 115 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mVariableUnits.

std::string AbstractOdeSystemInformation::GetSystemName ( ) const

Get the name of this system of ODEs.

Definition at line 52 of file AbstractOdeSystemInformation.cpp.

References mSystemName.

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

This method is used to establish whether a variable is in an ODE system's state vars, parameters or derived quantitites. You can then safely call GetAnyVariableIndex without a try...catch statement.

Parameters:

rName the name of a variable

Returns:: whether the variable is in this ODE system

Definition at line 193 of file AbstractOdeSystemInformation.cpp.

References HasDerivedQuantity(), HasParameter(), HasStateVariable(), and mInitialised.

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

Test whether this system has a particular named attribute.

Parameters:

rName the attribute name.

Definition at line 281 of file AbstractOdeSystemInformation.cpp.

References mAttributes, and mInitialised.

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

This method is used to establish whether a derived quantity is in an ODE system. You can then safely call GetDerivedQuantityIndex without a try...catch statement.

Parameters:

rName the name of a derived quantity

Returns:: whether the derived quantity is in this ODE system

Definition at line 252 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityNames, and mInitialised.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

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

This method is used to establish whether a parameter is in an ODE system. You can then safely call GetParameterIndex without a try...catch statement.

Parameters:

rName the name of a parameter

Returns:: whether the parameter is in this ODE system

Definition at line 148 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterNames.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

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

This method is used to establish whether a state variable is in an ODE system. You can then safely call GetStateVariableIndex without a try...catch statement.

Parameters:

rName the name of a state variable

Returns:: whether the state variable is in this ODE system

Definition at line 108 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableNames.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

virtual void AbstractOdeSystemInformation::Initialise ( ) [protected, pure virtual]

Initialise the ODE system information.

This must be provided by subclasses.

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

Get the vector of derived quantity names.

Definition at line 229 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityNames, and mInitialised.

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

Get the vector of derived quantity units.

Definition at line 235 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityUnits, and mInitialised.

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

Get the vector of parameter names.

Definition at line 125 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterNames.

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

Get the vector of parameter units.

Definition at line 131 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterUnits.

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

Get the state variable names vector.

Definition at line 85 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableNames.

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

Get the state variable units vector.

Definition at line 91 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableUnits.

void AbstractOdeSystemInformation::SetDefaultInitialCondition	(	unsigned	index,
		double	initialCondition
	)

Set a single component of the default initial conditions for the ODE system. This method DOES NOT change the state variables of the ODE 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 73 of file AbstractOdeSystemInformation.cpp.

References mInitialConditions, and mInitialised.

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

Set the default initial conditions for the ODE system. This method DOES NOT change the state variables of the ODE object on which it is called.

Parameters:

rInitialConditions vector containing initial values for the state variables

Definition at line 67 of file AbstractOdeSystemInformation.cpp.

References mInitialConditions, and mInitialised.

Member Data Documentation

std::map<std::string, double> AbstractOdeSystemInformation::mAttributes [protected]

Named attributes

Definition at line 95 of file AbstractOdeSystemInformation.hpp.

Referenced by GetAttribute(), GetNumberOfAttributes(), and HasAttribute().

std::vector<std::string> AbstractOdeSystemInformation::mDerivedQuantityNames [protected]

Derived quantity names

Definition at line 89 of file AbstractOdeSystemInformation.hpp.

Referenced by GetDerivedQuantityIndex(), HasDerivedQuantity(), and rGetDerivedQuantityNames().

std::vector<std::string> AbstractOdeSystemInformation::mDerivedQuantityUnits [protected]

Derived quantity units

Definition at line 92 of file AbstractOdeSystemInformation.hpp.

Referenced by GetAnyVariableUnits(), GetDerivedQuantityUnits(), GetNumberOfDerivedQuantities(), and rGetDerivedQuantityUnits().

std::string AbstractOdeSystemInformation::mFreeVariableName [protected]

The name of the free variable.

Definition at line 71 of file AbstractOdeSystemInformation.hpp.

Referenced by GetFreeVariableName().

std::string AbstractOdeSystemInformation::mFreeVariableUnits [protected]

The units of the free variable.

Definition at line 74 of file AbstractOdeSystemInformation.hpp.

Referenced by GetFreeVariableUnits().

std::vector<double> AbstractOdeSystemInformation::mInitialConditions [protected]

Suggested initial conditions

Definition at line 98 of file AbstractOdeSystemInformation.hpp.

Referenced by CombinedOdeSystemInformation::CombinedOdeSystemInformation(), GetInitialConditions(), SetDefaultInitialCondition(), and SetDefaultInitialConditions().

bool AbstractOdeSystemInformation::mInitialised [protected]

std::vector<std::string> AbstractOdeSystemInformation::mParameterNames [protected]

Parameter names

Definition at line 83 of file AbstractOdeSystemInformation.hpp.

Referenced by GetAnyVariableIndex(), GetParameterIndex(), HasParameter(), and rGetParameterNames().

std::vector<std::string> AbstractOdeSystemInformation::mParameterUnits [protected]

Parameter units

Definition at line 86 of file AbstractOdeSystemInformation.hpp.

Referenced by GetAnyVariableUnits(), GetNumberOfParameters(), GetParameterUnits(), and rGetParameterUnits().

std::string AbstractOdeSystemInformation::mSystemName [protected]

Human-friendly name for the ODE system

Definition at line 68 of file AbstractOdeSystemInformation.hpp.

Referenced by GetSystemName().

std::vector<std::string> AbstractOdeSystemInformation::mVariableNames [protected]

State variable names

Definition at line 77 of file AbstractOdeSystemInformation.hpp.

Referenced by CombinedOdeSystemInformation::CombinedOdeSystemInformation(), GetAnyVariableIndex(), GetStateVariableIndex(), HasStateVariable(), and rGetStateVariableNames().

std::vector<std::string> AbstractOdeSystemInformation::mVariableUnits [protected]

State variable units

Definition at line 80 of file AbstractOdeSystemInformation.hpp.

Referenced by CombinedOdeSystemInformation::CombinedOdeSystemInformation(), GetAnyVariableUnits(), GetStateVariableUnits(), and rGetStateVariableUnits().

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

ode/src/common/AbstractOdeSystemInformation.hpp
ode/src/common/AbstractOdeSystemInformation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation