A Runge-Kutta Fehlberg method for roadrunner. More...

#include <RK45Integrator.h>

Inheritance diagram for rr::RK45Integrator:

Public Member Functions
	RK45Integrator (ExecutableModel *m)
	Constructor: takes an executable model, does not own the pointer. More...

virtual	~RK45Integrator ()
	Destructor. More...

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

virtual double	integrate (double t, double h)
	implement Integrator interface More...

virtual void	restart (double t0)
	Restarts the integrator.

std::string	getName () const
	Get the name for this integrator. More...

std::string	getDescription () const
	Get the description for this integrator. More...

std::string	getHint () const
	Get the hint for this integrator. More...

Solver *	construct (ExecutableModel *executableModel) const
	Constructs a new Solver of a given type. More...

virtual Setting	getValue (std::string key)

IntegrationMethod	getIntegrationMethod () const
	Always deterministic for RK45. More...

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

virtual void	setListener (IntegratorListenerPtr)
	the integrator can hold a single listener. More...

virtual IntegratorListenerPtr	getListener ()
	get the integrator listener

	Integrator (ExecutableModel *model)

	Integrator ()

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

virtual void	loadConfigSettings ()

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

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...

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 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...

Static Public Member Functions
static std::string	getRK45Name ()
	Get the name for this integrator. More...

static std::string	getRK45Description ()
	Get the description for this integrator. More...

static std::string	getRK45Hint ()
	Get the hint for this integrator. More...

Additional Inherited Members
Public Types inherited from rr::Integrator
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 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)

Protected Attributes inherited from rr::Integrator
double	mIntegrationStartTime

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

Detailed Description

A Runge-Kutta Fehlberg method for roadrunner.

Author: KC

Uses the Fehlberg method, an adaptive step method, to integrate models.

Constructor & Destructor Documentation

◆ RK45Integrator()

rr::RK45Integrator::RK45Integrator ( ExecutableModel * m )

Constructor: takes an executable model, does not own the pointer.

Author: KC

◆ ~RK45Integrator()

rr::RK45Integrator::~RK45Integrator ( )

virtual

Destructor.

Author: KC

Member Function Documentation

◆ construct()

Solver * rr::RK45Integrator::construct ( ExecutableModel * model ) const

virtual

Constructs a new Solver of a given type.

Author: JKM, WBC

the caller is responsible for deleting memory associated with the returned Solver*.

Implements rr::Registrable.

◆ getDescription()

std::string rr::RK45Integrator::getDescription ( ) const

virtual

Get the description for this integrator.

Author: JKM

Note: Delegates to getDescription

Implements rr::Registrable.

◆ getHint()

std::string rr::RK45Integrator::getHint ( ) const

virtual

Get the hint for this integrator.

Author: WBC

Note: Delegates to getHint

Implements rr::Registrable.

◆ getIntegrationMethod()

Integrator::IntegrationMethod rr::RK45Integrator::getIntegrationMethod ( ) const

virtual

Always deterministic for RK45.

Author: JKM

Implements rr::Integrator.

◆ getName()

std::string rr::RK45Integrator::getName ( ) const

virtual

Get the name for this integrator.

Author: JKM

Note: Delegates to getName

Implements rr::Registrable.

◆ getRK45Description()

std::string rr::RK45Integrator::getRK45Description ( )

static

Get the description for this integrator.

Author: JKM

◆ getRK45Hint()

std::string rr::RK45Integrator::getRK45Hint ( )

static

Get the hint for this integrator.

Author: JKM

◆ getRK45Name()

std::string rr::RK45Integrator::getRK45Name ( )

static

Get the name for this integrator.

Author: JKM

◆ integrate()

double rr::RK45Integrator::integrate	(	double	t,
		double	h
	)

virtual

implement Integrator interface

Author: CC

Integrates the model from t to t + h.

Attempts to find the state std::vector at t + h, and returns time t + h if successful. If the integrator does not find a convergent solution, the state std::vector is not updated and t is returned. Also calculates a new timestep and saves it to a member variable for future use.

Implements rr::Integrator.

◆ resetSettings()

void rr::RK45Integrator::resetSettings ( )

virtual

Reset all integrator settings to their respective default values.

Author: JKM

Reimplemented from rr::Solver.

◆ setListener()

void rr::RK45Integrator::setListener ( IntegratorListenerPtr )

virtual

the integrator can hold a single listener.

If clients require multicast, they can create a multi-cast listener.

Implements rr::Integrator.

◆ syncWithModel()

void rr::RK45Integrator::syncWithModel ( ExecutableModel * m )

virtual

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

Author: JKM

Reimplemented from rr::Integrator.

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

RK45Integrator.h
RK45Integrator.cpp

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RK45Integrator()

◆ ~RK45Integrator()

Member Function Documentation

◆ construct()

◆ getDescription()

◆ getHint()

◆ getIntegrationMethod()

◆ getName()

◆ getRK45Description()

◆ getRK45Hint()

◆ getRK45Name()

◆ integrate()

◆ resetSettings()

◆ setListener()

◆ syncWithModel()