Integrator is an abstract base class that provides an interface to specific integrator class implementations. More...

#include <Integrator.h>

Inheritance diagram for rr::Integrator:

Public Types
enum	IntegrationMethod { Deterministic , Stochastic , Hybrid , Other }

Public Types inherited from rr::Solver
using	SettingsList = std::vector< std::string >

using	SettingsMap = std::unordered_map< std::string, Setting >

using	DisplayNameMap = std::unordered_map< std::string, std::string >

using	HintMap = std::unordered_map< std::string, std::string >

using	DescriptionMap = std::unordered_map< std::string, std::string >

Public Member Functions
	Integrator (ExecutableModel *model)

virtual IntegrationMethod	getIntegrationMethod () const =0

virtual void	syncWithModel (ExecutableModel *m)
	Called whenever a new model is loaded to allow integrator to reset internal state. More...

virtual void	loadConfigSettings ()

virtual void	loadSBMLSettings (const std::string &filename)

virtual double	integrate (double t0, double hstep)=0

virtual void	restart (double t0)=0

virtual void	tweakTolerances ()
	Fix tolerances for SBML tests. More...

virtual void	setIndividualTolerance (std::string sid, double value)
	Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator. More...

virtual std::vector< double >	getAbsoluteToleranceVector ()
	Get the absolute tolerance vector for the solver. More...

virtual void	setListener (IntegratorListenerPtr)=0

virtual IntegratorListenerPtr	getListener ()=0

std::string	toString () const
	Return a std::string representation of the solver. More...

virtual std::string	toRepr () const
	Return std::string representation a la Python repr method. More...

void	setIntegrationStartTime (double time)

	Solver ()=default

	Solver (ExecutableModel *model)

virtual void	setValue (const std::string &key, Setting value)
	Pull down the setValue from superclass. More...

Public Member Functions inherited from rr::Solver
	Solver (ExecutableModel *model)

void	updateSettings (Dictionary *inputSettings)
	Update settings values. More...

std::vector< std::string >	getSettings () const
	Get a list of all settings for this solver. More...

std::unordered_map< std::string, Setting > &	getSettingsMap ()
	get settings for this solver More...

virtual void	resetSettings ()
	Reset all settings to their respective default values.

virtual Setting	getValue (const std::string &key) const
	Get the value of an integrator setting. More...

virtual Setting	hasValue (const std::string &key) const
	Return true if this setting is supported by the integrator. More...

virtual size_t	getNumParams () const
	Get the number of parameters. More...

virtual std::string	getParamName (size_t n) const
	Get the name of the parameter at index n. More...

virtual std::string	getParamDisplayName (int n) const
	Get the display name of the parameter at index n. More...

virtual std::string	getParamHint (int n) const
	Get the hint of the parameter at index n. More...

virtual std::string	getParamDesc (int n) const
	Get the description of the parameter at index n. More...

virtual std::string	getValueAsString (const std::string &key)
	Wrapper for getValue which converts output to a specific type. More...

virtual void	setValue (const std::string &key, Setting value)

virtual std::string	getSettingsRepr () const
	Get the solver settings as a std::string. More...

virtual std::string	settingsPyDictRepr () const
	Python dictionary-style std::string representation of settings. More...

const std::string &	getDisplayName (const std::string &key) const
	Gets the hint associated with a given key. More...

const std::string &	getHint (const std::string &key) const
	Gets the hint associated with a given key. More...

const std::string &	getDescription (const std::string &key) const
	Gets the description associated with a given key. More...

Setting::TypeId	getType (const std::string &key) const
	Gets the type associated with a given key. More...

virtual ExecutableModel *	getModel () const
	returns the pointer to the ExecutableModel

virtual std::string	getName () const=0
	Gets the name associated with this Solver type. More...

virtual std::string	getHint () const=0
	Gets the hint associated with this Solver type. More...

virtual std::string	getDescription () const=0
	Gets the description associated with this Solver type. More...

Public Member Functions inherited from rr::Registrable
virtual std::string	getName () const =0
	Gets the name associated with this Solver type. More...

virtual std::string	getDescription () const =0
	Gets the description associated with this Solver type. More...

virtual std::string	getHint () const =0
	Gets the hint associated with this Solver type. More...

virtual Solver *	construct (ExecutableModel *model) const =0
	Constructs a new Solver of a given type. More...

Protected Attributes
double	mIntegrationStartTime

Protected Attributes inherited from rr::Solver
ExecutableModel *	mModel = nullptr
	non-owning pointer to model

Additional Inherited Members
Public Attributes inherited from rr::Solver
SettingsList	sorted_settings

SettingsMap	settings

DisplayNameMap	display_names_

HintMap	hints

DescriptionMap	descriptions

Protected Member Functions inherited from rr::Solver
void	addSetting (const std::string &name, const Setting &val, const std::string &display_name, const std::string &hint, const std::string &description)

Detailed Description

Integrator is an abstract base class that provides an interface to specific integrator class implementations.

Member Function Documentation

◆ getAbsoluteToleranceVector()

std::vector< double > rr::Integrator::getAbsoluteToleranceVector ( )

virtual

Get the absolute tolerance vector for the solver.

Most solvers do not have absolute tolerances; this retrieves the vector for the ones (like CVODE) that do.

Reimplemented in rr::CVODEIntegrator.

◆ setIndividualTolerance()

void rr::Integrator::setIndividualTolerance	(	std::string	sid,
		double	value
	)

virtual

Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator.

Author: FY

Reimplemented in rr::CVODEIntegrator.

◆ setValue()

void rr::Solver::setValue

Pull down the setValue from superclass.

We do not need to reimplement this but we make it explicit.

◆ syncWithModel()

void rr::Integrator::syncWithModel ( ExecutableModel * m )

virtual

Called whenever a new model is loaded to allow integrator to reset internal state.

Author: JKM

Implements rr::Solver.

Reimplemented in rr::RK4Integrator, rr::GillespieIntegrator, rr::CVODEIntegrator, and rr::RK45Integrator.

◆ toRepr()

std::string rr::Integrator::toRepr ( ) const

virtual

Return std::string representation a la Python repr method.

Author: JKM

Reimplemented from rr::Solver.

Reimplemented in rr::EulerIntegrator.

◆ toString()

std::string rr::Integrator::toString ( ) const

virtual

Return a std::string representation of the solver.

Author: JKM

Reimplemented from rr::Solver.

◆ tweakTolerances()

void rr::Integrator::tweakTolerances ( )

virtual

Fix tolerances for SBML tests.

Author: JKM, WBC, ETS, MTK

In order to ensure that the results of the SBML test suite remain valid, this method enforces a lower bound on tolerance values. Sets minimum absolute and relative tolerances to Config::CVODE_MIN_ABSOLUTE and Config::CVODE_MIN_RELATIVE resp.

Reimplemented in rr::CVODEIntegrator.

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

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ getAbsoluteToleranceVector()

◆ setIndividualTolerance()

◆ setValue()

◆ syncWithModel()

◆ toRepr()

◆ toString()

◆ tweakTolerances()