#include <CombinedOdeSystem.hpp>

Inheritance diagram for CombinedOdeSystem:

Collaboration diagram for CombinedOdeSystem:

Classes
struct	VariableParameterMap

Public Member Functions
	CombinedOdeSystem (std::vector< AbstractOdeSystem * > odeSystems)

void	Configure (const std::map< unsigned, unsigned > &rVariableParameterMap, AbstractOdeSystem pVariableOdeSystem, AbstractOdeSystem pParameterOdeSystem)

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

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

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

Private Attributes
std::vector< AbstractOdeSystem * >	mOdeSystems

std::vector< std::vector< double > >	mWorkingStateVars

std::vector< std::vector< double > >	mWorkingDerivs

std::vector< unsigned >	mOffsets

std::vector< struct VariableParameterMap >	mVariableParameterMaps

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)

Protected Attributes inherited from AbstractOdeSystem
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

Detailed Description

An ODE system formed by combining several subsystems.

Instances of this class are formed by passing other ODE system instances to our constructor, and then calling Configure to set up any coupling between subsystems. This allows state variables from one system to be used as parameters in other systems.

This allows us to set up coupled systems such as $dy/dt = f(y, t)$ from subsystems $dy_1/dt = f_1(y_1, t; y_2)$ and $dy_2/dt = f_2(y_2, t; y_1)$ where $y = (y_1, y_2)$ .

The vector of state variables for the combined system is formed as the concatenation of the state variable vectors of the subsystem. This class also makes use of the CombinedOdeSystemInformation class to provide initial conditions, etc.

Definition at line 66 of file CombinedOdeSystem.hpp.

Constructor & Destructor Documentation

◆ CombinedOdeSystem()

CombinedOdeSystem::CombinedOdeSystem ( std::vector< AbstractOdeSystem * > odeSystems )

Create a combined ODE system from a vector of subsystems.

Parameters

odeSystems the subsystems.

Definition at line 40 of file CombinedOdeSystem.cpp.

References CombinedOdeSystemInformation::Instance(), AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, mOdeSystems, mOffsets, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mWorkingDerivs, mWorkingStateVars, and AbstractParameterisedSystem< std::vector< double > >::ResetToInitialConditions().

Member Function Documentation

◆ Configure()

void CombinedOdeSystem::Configure	(	const std::map< unsigned, unsigned > &	rVariableParameterMap,
		AbstractOdeSystem *	pVariableOdeSystem,
		AbstractOdeSystem *	pParameterOdeSystem
	)

Configure a mapping between the state variables of one subsystem and the parameters of another.

Parameters

rVariableParameterMap	a map specifying which state variables (keys) are mapped to which parameters (values).
pVariableOdeSystem	the ODE subsystem providing state variable values.
pParameterOdeSystem	the ODE subsystem whose parameters should be set.

Definition at line 67 of file CombinedOdeSystem.cpp.

References mOdeSystems, mVariableParameterMaps, CombinedOdeSystem::VariableParameterMap::pParameterOdeSystem, CombinedOdeSystem::VariableParameterMap::pVariableOdeSystemIndex, and CombinedOdeSystem::VariableParameterMap::theMap.

◆ EvaluateYDerivatives()

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

virtual

Evaluate the right-hand side of the combined system.

This calls EvaluateYDerivatives for each subsystem with the appropriate portion of rY and rDY, having set parameters from values in rY according to the configured maps.

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

Implements AbstractOdeSystem.

Definition at line 85 of file CombinedOdeSystem.cpp.

References mOdeSystems, mOffsets, mVariableParameterMaps, mWorkingDerivs, mWorkingStateVars, and AbstractParameterisedSystem< VECTOR >::SetParameter().

Member Data Documentation

◆ mOdeSystems

std::vector<AbstractOdeSystem*> CombinedOdeSystem::mOdeSystems

private

The subsystems forming this combined system.

Definition at line 71 of file CombinedOdeSystem.hpp.

Referenced by CombinedOdeSystem(), Configure(), and EvaluateYDerivatives().

◆ mOffsets

std::vector<unsigned> CombinedOdeSystem::mOffsets

private

Keeps track of where the state variable vector for each subsystem is located within the combined state variable vector.

Definition at line 81 of file CombinedOdeSystem.hpp.

Referenced by CombinedOdeSystem(), and EvaluateYDerivatives().

◆ mVariableParameterMaps

std::vector<struct VariableParameterMap> CombinedOdeSystem::mVariableParameterMaps

private

Stores the information passed to Configure calls.

Definition at line 104 of file CombinedOdeSystem.hpp.

Referenced by Configure(), and EvaluateYDerivatives().

◆ mWorkingDerivs

std::vector<std::vector<double> > CombinedOdeSystem::mWorkingDerivs

private

Working memory for the DY vectors of the subsystems.

Definition at line 76 of file CombinedOdeSystem.hpp.

Referenced by CombinedOdeSystem(), and EvaluateYDerivatives().

◆ mWorkingStateVars

std::vector<std::vector<double> > CombinedOdeSystem::mWorkingStateVars

private

Working memory for the Y vectors of the subsystems.

Definition at line 74 of file CombinedOdeSystem.hpp.

Referenced by CombinedOdeSystem(), and EvaluateYDerivatives().

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

ode/src/common/CombinedOdeSystem.hpp
ode/src/common/CombinedOdeSystem.cpp

Classes

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CombinedOdeSystem()

Member Function Documentation

◆ Configure()

◆ EvaluateYDerivatives()

Member Data Documentation

◆ mOdeSystems

◆ mOffsets

◆ mVariableParameterMaps

◆ mWorkingDerivs

◆ mWorkingStateVars