A RoadRunner integrator based on CVODE; serves as RoadRunner's main integrator for ODEs. More...

#include <CVODEIntegrator.h>

Inheritance diagram for rr::CVODEIntegrator:

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

	~CVODEIntegrator () override
	Destructor. More...

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

void	loadConfigSettings () override

void	loadSBMLSettings (const std::string &filename) override
	Load an SBML settings file and apply the configuration options. More...

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

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

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

IntegrationMethod	getIntegrationMethod () const override
	Always deterministic for CVODE. More...

void	setValue (std::string setting, const Variant &value) override
	Sets the value of an integrator setting (e.g. absolute_tolerance) More...

void	setIndividualTolerance (string sid, double value) override
	Sets tolerance for individual species. More...

void	setConcentrationTolerance (const Variant &value) override
	Sets tolerance based on concentration of species. More...

std::vector< double >	getConcentrationTolerance () override
	Gets tolerance based on concentration of species. More...

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

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

double	integrate (double t0, double tf) override
	Main integration routine. More...

void	restart (double timeStart) override
	Reset time to zero and reinitialize model. More...

IntegratorListenerPtr	getListener () override
	Gets the integrator listener. More...

void	setListener (IntegratorListenerPtr) override
	Sets the integrator listener. More...

void	checkType () const
	Does a RT type check which throws if it fails, EVEN IF RTTI IS DISABLED. More...

void	checkVectorSize (int expected, size_t real) const
	Does a size check which throws if it fails. More...

void	checkIndex (int index, int size) const
	Does a index check which throws if it is out of bound. More...

std::string	ToString (int val) const
	Converts integer to string for error print. More...

std::string	ToString (size_t val) const
	Converts size_t to string for error print. More...

std::string	cvodeDecodeError (int cvodeError, bool exInfo=true)
	decode the cvode error code to a string

N_Vector	getStateVector () const
	getter for the internal state vector More...

SUNNonlinearSolver	getSolver () const
	getter for the internal Sundials linear solver object More...

void *	getCvodeMemory () const
	getter for the internal CVode memory buffer More...

Public Member Functions inherited from rr::Integrator
std::string	toString () const
	Return a string representation of the solver. More...

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

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

Public Member Functions inherited from rr::Solver
std::vector< std::string >	getSettings () const
	Get a list of all settings for this solver. More...

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

virtual Variant	hasValue (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 int	getValueAsInt (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual unsigned int	getValueAsUInt (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual long	getValueAsLong (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual unsigned long	getValueAsULong (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual float	getValueAsFloat (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual double	getValueAsDouble (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual std::vector< double >	getValueAsDoubleVector (std::string key)
	Wrapper for getValue which converts output to a specific type.

virtual char	getValueAsChar (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

virtual unsigned char	getValueAsUChar (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

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

virtual bool	getValueAsBool (std::string key)
	Wrapper for getValue which converts output to a specific type. More...

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

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

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

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

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

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

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

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

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

Friends
int	cvodeDyDtFcn (double t, N_Vector cv_y, N_Vector cv_ydot, void *f_data)

int	cvodeRootFcn (double t, N_Vector y, double gout, void g_data)

Additional Inherited Members
Public Types inherited from rr::Integrator
enum	IntegrationMethod { Deterministic , Stochastic , Hybrid , Other }

Protected Types inherited from rr::Solver
typedef std::vector< std::string >	SettingsList

typedef RR_UNORDERED_MAP< std::string, Variant >	SettingsMap

typedef RR_UNORDERED_MAP< std::string, std::string >	DisplayNameMap

typedef RR_UNORDERED_MAP< std::string, std::string >	HintMap

typedef RR_UNORDERED_MAP< std::string, std::string >	DescriptionMap

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

Protected Attributes inherited from rr::Solver
SettingsList	sorted_settings

SettingsMap	settings

DisplayNameMap	display_names_

HintMap	hints

DescriptionMap	descriptions

Detailed Description

A RoadRunner integrator based on CVODE; serves as RoadRunner's main integrator for ODEs.

Author: WBC, ETS, MTK

Provides a wrapper around CVODE from the SUNDIALS suite. CVODE has two main solvers: an Adams-Moulton solver for non-stiff problems, and a backward differentiation formula (BDF) solver for stiff problems. See: https://computation.llnl.gov/casc/sundials/documentation/toms_sundials.pdf

Constructor & Destructor Documentation

◆ CVODEIntegrator()

rr::CVODEIntegrator::CVODEIntegrator ( ExecutableModel * oModel )

explicit

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

Author: WBC, ETS, MTK

◆ ~CVODEIntegrator()

rr::CVODEIntegrator::~CVODEIntegrator ( )

override

Destructor.

Author: WBC, ETS, MTK

Member Function Documentation

◆ checkIndex()

void rr::CVODEIntegrator::checkIndex	(	int	index,
		int	size
	)		const

Does a index check which throws if it is out of bound.

Author: FY

◆ checkType()

void rr::CVODEIntegrator::checkType ( ) const

Does a RT type check which throws if it fails, EVEN IF RTTI IS DISABLED.

Author: JKM

◆ checkVectorSize()

void rr::CVODEIntegrator::checkVectorSize	(	int	expected,
		size_t	real
	)		const

Does a size check which throws if it fails.

Author: FY

◆ getConcentrationTolerance()

std::vector<double> rr::CVODEIntegrator::getConcentrationTolerance ( )

overridevirtual

Gets tolerance based on concentration of species.

Author: FY

Reimplemented from rr::Integrator.

◆ getCVODEIntegratorDescription()

static std::string rr::CVODEIntegrator::getCVODEIntegratorDescription ( )

static

Get the description for this integrator.

Author: JKM

◆ getCVODEIntegratorHint()

static std::string rr::CVODEIntegrator::getCVODEIntegratorHint ( )

static

Get the hint for this integrator.

Author: JKM

◆ getCVODEIntegratorName()

static std::string rr::CVODEIntegrator::getCVODEIntegratorName ( )

static

Get the name for this integrator.

Author: JKM

◆ getCvodeMemory()

void* rr::CVODEIntegrator::getCvodeMemory ( ) const

getter for the internal CVode memory buffer

Author: CW

Note: This method was created to enable external access (mostly for tests) to the Sundials memory buffer object. This method should not be exposed at the Python level.

◆ getDescription()

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

overridevirtual

Get the description for this integrator.

Author: WBC

Note: Delegates to getDescription

Implements rr::Solver.

◆ getHint()

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

overridevirtual

Get the hint for this integrator.

Author: WBC

Note: Delegates to getHint

Implements rr::Solver.

◆ getIntegrationMethod()

IntegrationMethod rr::CVODEIntegrator::getIntegrationMethod ( ) const

overridevirtual

Always deterministic for CVODE.

Author: WBC, ETS, MTK

Implements rr::Integrator.

◆ getListener()

IntegratorListenerPtr rr::CVODEIntegrator::getListener ( )

overridevirtual

Gets the integrator listener.

Author: WBC, ETS

Implements rr::Integrator.

◆ getName()

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

overridevirtual

Get the name for this integrator.

Author: WBC

Note: Delegates to getName

Implements rr::Solver.

◆ getSolver()

SUNNonlinearSolver rr::CVODEIntegrator::getSolver ( ) const

getter for the internal Sundials linear solver object

Author: CW

Note: This method was created to enable external access (mostly for tests) to the Sundials SUNLinearSolver object. This method should not be exposed at the Python level.

◆ getStateVector()

N_Vector rr::CVODEIntegrator::getStateVector ( ) const

getter for the internal state vector

Author: CW

Note: This method was created to enable external access (mostly for tests) to the Sundials N_Vector object. This method should not be exposed at the Python level.

◆ integrate()

double rr::CVODEIntegrator::integrate	(	double	t0,
		double	tf
	)

overridevirtual

Main integration routine.

Author: WBC, ETS, MTK

Implements rr::Integrator.

◆ loadSBMLSettings()

void rr::CVODEIntegrator::loadSBMLSettings ( const std::string & filename )

overridevirtual

Load an SBML settings file and apply the configuration options.

Author: WBC

Note: Can assign relative and absolute tolerances

Reimplemented from rr::Integrator.

◆ resetSettings()

void rr::CVODEIntegrator::resetSettings ( )

overridevirtual

Reset all integrator settings to their respective default values.

Author: JKM

Reimplemented from rr::Solver.

◆ restart()

void rr::CVODEIntegrator::restart ( double timeStart )

overridevirtual

Reset time to zero and reinitialize model.

Author: WBC, ETS, MTK

Applies events which occur before time zero. Reinitializes CVODE and the executable model.

Implements rr::Integrator.

◆ setConcentrationTolerance()

void rr::CVODEIntegrator::setConcentrationTolerance ( const Variant & value )

overridevirtual

Sets tolerance based on concentration of species.

Author: FY

First converts the concentration tolerances to amount tolerances by multiplying the compartment volume of species. Whichever is smaller will be stored as absolute_tolerance and used in the integration process.

Reimplemented from rr::Integrator.

◆ setIndividualTolerance()

void rr::CVODEIntegrator::setIndividualTolerance	(	string	sid,
		double	value
	)

overridevirtual

Sets tolerance for individual species.

Author: FY

Reimplemented from rr::Integrator.

◆ setListener()

void rr::CVODEIntegrator::setListener ( IntegratorListenerPtr )

overridevirtual

Sets the integrator listener.

Author: WBC, ETS

Implements rr::Integrator.

◆ setValue()

void rr::CVODEIntegrator::setValue	(	std::string	setting,
		const Variant &	value
	)

overridevirtual

Sets the value of an integrator setting (e.g. absolute_tolerance)

Author: WBC, ETS, MTK

Reimplemented from rr::Solver.

◆ syncWithModel()

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

overridevirtual

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

Author: JKM

Reimplemented from rr::Integrator.

◆ ToString() [1/2]

std::string rr::CVODEIntegrator::ToString ( int val ) const

Converts integer to string for error print.

Author: FY

◆ ToString() [2/2]

std::string rr::CVODEIntegrator::ToString ( size_t val ) const

Converts size_t to string for error print.

Author: LPS

◆ tweakTolerances()

void rr::CVODEIntegrator::tweakTolerances ( )

overridevirtual

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 from rr::Integrator.

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

CVODEIntegrator.h

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CVODEIntegrator()

◆ ~CVODEIntegrator()

Member Function Documentation

◆ checkIndex()

◆ checkType()

◆ checkVectorSize()

◆ getConcentrationTolerance()

◆ getCVODEIntegratorDescription()

◆ getCVODEIntegratorHint()

◆ getCVODEIntegratorName()

◆ getCvodeMemory()

◆ getDescription()

◆ getHint()

◆ getIntegrationMethod()

◆ getListener()

◆ getName()

◆ getSolver()

◆ getStateVector()

◆ integrate()

◆ loadSBMLSettings()

◆ resetSettings()

◆ restart()

◆ setConcentrationTolerance()

◆ setIndividualTolerance()

◆ setListener()

◆ setValue()

◆ syncWithModel()

◆ ToString() [1/2]

◆ ToString() [2/2]

◆ tweakTolerances()