Wrapper class for 'cvodes' integrator from LLNL. More...

#include <CVodesIntegrator.h>

Inheritance diagram for CVodesIntegrator:

Detailed Description

Wrapper class for 'cvodes' integrator from LLNL.

See FuncEval.h. Classes that use CVodesIntegrator: ImplicitSurfChem, ReactorNet

Definition at line 26 of file CVodesIntegrator.h.

Public Member Functions
	CVodesIntegrator ()
	Constructor.

void	setTolerances (double reltol, size_t n, double *abstol) override
	Set error tolerances.

void	setTolerances (double reltol, double abstol) override
	Set error tolerances.

void	setSensitivityTolerances (double reltol, double abstol) override
	Set the sensitivity error tolerances.

void	initialize (double t0, FuncEval &func) override
	Initialize the integrator for a new problem.

void	reinitialize (double t0, FuncEval &func) override

void	integrate (double tout) override
	Integrate the system of equations.

double	step (double tout) override
	Integrate the system of equations.

double &	solution (size_t k) override
	The current value of the solution of equation k.

double *	solution () override
	The current value of the solution of the system of equations.

double *	derivative (double tout, int n) override
	n-th derivative of the output function at time tout.

int	lastOrder () const override
	Order used during the last solution step.

int	nEquations () const override
	The number of equations.

int	nEvals () const override
	The number of function evaluations.

void	setMaxOrder (int n) override
	Set the maximum integration order that will be used.

void	setMethod (MethodType t) override
	Set the solution method.

void	setMaxStepSize (double hmax) override
	Set the maximum step size.

void	setMinStepSize (double hmin) override
	Set the minimum step size.

void	setMaxSteps (int nmax) override
	Set the maximum number of time-steps the integrator can take before reaching the next output time.

int	maxSteps () override
	Returns the maximum number of time-steps the integrator can take before reaching the next output time.

void	setMaxErrTestFails (int n) override
	Set the maximum permissible number of error test failures.

AnyMap	solverStats () const override
	Get solver stats from integrator.

void	setLinearSolverType (const string &linSolverType) override
	Set the linear solver type.

string	linearSolverType () const override
	Return the integrator problem type.

void	setBandwidth (int N_Upper, int N_Lower) override

int	nSensParams () override

double	sensitivity (size_t k, size_t p) override

void	setProblemType (int probtype) override
	Set the problem type.

string	getErrorInfo (int N)
	Returns a string listing the weighted error estimates associated with each solution component.

Public Member Functions inherited from Integrator
	Integrator ()
	Default Constructor.

virtual	~Integrator ()
	Destructor.

virtual void	setTolerances (double reltol, size_t n, double *abstol)
	Set error tolerances.

virtual void	setTolerances (double reltol, double abstol)
	Set error tolerances.

virtual void	setSensitivityTolerances (double reltol, double abstol)
	Set the sensitivity error tolerances.

virtual void	setProblemType (int probtype)
	Set the problem type.

virtual void	setLinearSolverType (const string &linSolverType)
	Set the linear solver type.

virtual void	setPreconditioner (shared_ptr< PreconditionerBase > preconditioner)
	Set preconditioner used by the linear solver.

virtual void	preconditionerSolve (size_t stateSize, double rhs, double output)
	Solve a linear system Ax=b where A is the preconditioner.

virtual PreconditionerSide	preconditionerSide ()
	Return the side of the system on which the preconditioner is applied.

virtual shared_ptr< PreconditionerBase >	preconditioner ()
	Return preconditioner reference to object.

virtual string	linearSolverType () const
	Return the integrator problem type.

virtual void	initialize (double t0, FuncEval &func)
	Initialize the integrator for a new problem.

virtual void	reinitialize (double t0, FuncEval &func)

virtual void	integrate (double tout)
	Integrate the system of equations.

virtual double	step (double tout)
	Integrate the system of equations.

virtual double &	solution (size_t k)
	The current value of the solution of equation k.

virtual double *	solution ()
	The current value of the solution of the system of equations.

virtual double *	derivative (double tout, int n)
	n-th derivative of the output function at time tout.

virtual int	lastOrder () const
	Order used during the last solution step.

virtual int	nEquations () const
	The number of equations.

virtual int	nEvals () const
	The number of function evaluations.

virtual int	maxOrder () const

virtual void	setMaxOrder (int n)
	Set the maximum integration order that will be used.

virtual void	setMethod (MethodType t)
	Set the solution method.

virtual void	setMaxStepSize (double hmax)
	Set the maximum step size.

virtual void	setMinStepSize (double hmin)
	Set the minimum step size.

virtual void	setMaxErrTestFails (int n)
	Set the maximum permissible number of error test failures.

virtual void	setMaxSteps (int nmax)
	Set the maximum number of time-steps the integrator can take before reaching the next output time.

virtual int	maxSteps ()
	Returns the maximum number of time-steps the integrator can take before reaching the next output time.

virtual void	setBandwidth (int N_Upper, int N_Lower)

virtual int	nSensParams ()

virtual double	sensitivity (size_t k, size_t p)

virtual AnyMap	solverStats () const
	Get solver stats from integrator.

virtual int	maxNonlinIterations () const

virtual void	setMaxNonlinIterations (int n)

virtual int	maxNonlinConvFailures () const

virtual void	setMaxNonlinConvFailures (int n)

virtual bool	algebraicInErrorTest () const

virtual void	includeAlgebraicInErrorTest (bool yesno)

Public Attributes
string	m_error_message
	Error message information provide by CVodes.

Protected Member Functions
void	applyOptions ()
	Applies user-specified options to the underlying CVODES solver.

Private Member Functions
void	sensInit (double t0, FuncEval &func)

void	checkError (long flag, const string &ctMethod, const string &cvodesMethod) const
	Check whether a CVODES method indicated an error.

Private Attributes
size_t	m_neq = 0

void *	m_cvode_mem = nullptr

SundialsContext	m_sundials_ctx
	SUNContext object for Sundials>=6.0.

void *	m_linsol = nullptr
	Sundials linear solver object.

void *	m_linsol_matrix = nullptr
	matrix used by Sundials

FuncEval *	m_func = nullptr

double	m_t0 = 0.0

double	m_time
	The current system time, corresponding to m_y.

double	m_tInteg
	The latest time reached by the integrator. May be greater than m_time.

N_Vector	m_y = nullptr
	The system state at m_time.

N_Vector	m_abstol = nullptr

N_Vector	m_dky = nullptr

string	m_type = "DENSE"

int	m_itol

int	m_method

int	m_maxord = 0

double	m_reltol = 1e-9

double	m_abstols = 1e-15

double	m_reltolsens = 1e-5

double	m_abstolsens = 1e-4

size_t	m_nabs = 0

double	m_hmax = 0.0

double	m_hmin = 0.0

int	m_maxsteps = 20000

int	m_maxErrTestFails = 0

N_Vector *	m_yS = nullptr

size_t	m_np = 0

int	m_mupper = 0

int	m_mlower = 0

bool	m_sens_ok = false
	Indicates whether the sensitivities stored in m_yS have been updated for at the current integrator time.

Additional Inherited Members
Protected Attributes inherited from Integrator
shared_ptr< PreconditionerBase >	m_preconditioner
	Pointer to preconditioner object used in integration which is set by setPreconditioner and initialized inside of ReactorNet::initialize()

PreconditionerSide	m_prec_side = PreconditionerSide::NO_PRECONDITION
	Type of preconditioning used in applyOptions.

Constructor & Destructor Documentation

◆ CVodesIntegrator()

CVodesIntegrator ( )

Constructor.

Default settings: dense Jacobian, no user-supplied Jacobian function, Newton iteration.

Definition at line 79 of file CVodesIntegrator.cpp.

◆ ~CVodesIntegrator()

~CVodesIntegrator ( )

override

Definition at line 85 of file CVodesIntegrator.cpp.

Member Function Documentation

◆ setTolerances() [1/2]

void setTolerances	(	double	reltol,
		size_t	n,
		double *	abstol
	)

overridevirtual

Set error tolerances.

Parameters

reltol	scalar relative tolerance
n	Number of equations
abstol	array of N absolute tolerance values

Reimplemented from Integrator.

Definition at line 126 of file CVodesIntegrator.cpp.

◆ setTolerances() [2/2]

void setTolerances	(	double	reltol,
		double	abstol
	)

overridevirtual

Set error tolerances.

Parameters

reltol	scalar relative tolerance
abstol	scalar absolute tolerance

Reimplemented from Integrator.

Definition at line 142 of file CVodesIntegrator.cpp.

◆ setSensitivityTolerances()

void setSensitivityTolerances	(	double	reltol,
		double	abstol
	)

overridevirtual

Set the sensitivity error tolerances.

Parameters

reltol	scalar relative tolerance
abstol	scalar absolute tolerance

Reimplemented from Integrator.

Definition at line 149 of file CVodesIntegrator.cpp.

◆ initialize()

void initialize	(	double	t0,
		FuncEval &	func
	)

overridevirtual

Initialize the integrator for a new problem.

Call after all options have been set.

Parameters

t0	initial time
func	RHS evaluator object for system of equations.

Reimplemented from Integrator.

Definition at line 251 of file CVodesIntegrator.cpp.

◆ reinitialize()

void reinitialize	(	double	t0,
		FuncEval &	func
	)

overridevirtual

Reimplemented from Integrator.

Definition at line 335 of file CVodesIntegrator.cpp.

◆ integrate()

void integrate ( double tout )

overridevirtual

Integrate the system of equations.

Parameters

tout	Integrate to this time. Note that this is the absolute time value, not a time interval.

Reimplemented from Integrator.

Definition at line 495 of file CVodesIntegrator.cpp.

◆ step()

double step ( double tout )

overridevirtual

Integrate the system of equations.

Parameters

tout	integrate to this time. Note that this is the absolute time value, not a time interval.

Reimplemented from Integrator.

Definition at line 533 of file CVodesIntegrator.cpp.

◆ solution() [1/2]

double & solution ( size_t k )

overridevirtual

The current value of the solution of equation k.

Reimplemented from Integrator.

Definition at line 116 of file CVodesIntegrator.cpp.

◆ solution() [2/2]

double * solution ( )

overridevirtual

The current value of the solution of the system of equations.

Reimplemented from Integrator.

Definition at line 121 of file CVodesIntegrator.cpp.

◆ derivative()

double * derivative	(	double	tout,
		int	n
	)

overridevirtual

n-th derivative of the output function at time tout.

Reimplemented from Integrator.

Definition at line 553 of file CVodesIntegrator.cpp.

◆ lastOrder()

int lastOrder ( ) const

overridevirtual

Order used during the last solution step.

Reimplemented from Integrator.

Definition at line 560 of file CVodesIntegrator.cpp.

◆ nEquations()

int nEquations ( ) const

inlineoverridevirtual

The number of equations.

Reimplemented from Integrator.

Definition at line 46 of file CVodesIntegrator.h.

◆ nEvals()

int nEvals ( ) const

overridevirtual

The number of function evaluations.

Reimplemented from Integrator.

Definition at line 567 of file CVodesIntegrator.cpp.

◆ setMaxOrder()

void setMaxOrder ( int n )

inlineoverridevirtual

Set the maximum integration order that will be used.

Reimplemented from Integrator.

Definition at line 50 of file CVodesIntegrator.h.

◆ setMethod()

void setMethod ( MethodType t )

overridevirtual

Set the solution method.

Reimplemented from Integrator.

Definition at line 173 of file CVodesIntegrator.cpp.

◆ setMaxStepSize()

void setMaxStepSize ( double hmax )

overridevirtual

Set the maximum step size.

Reimplemented from Integrator.

Definition at line 184 of file CVodesIntegrator.cpp.

◆ setMinStepSize()

void setMinStepSize ( double hmin )

overridevirtual

Set the minimum step size.

Reimplemented from Integrator.

Definition at line 192 of file CVodesIntegrator.cpp.

◆ setMaxSteps()

void setMaxSteps ( int nmax )

overridevirtual

Set the maximum number of time-steps the integrator can take before reaching the next output time.

Parameters

nmax	The maximum number of steps, setting this value to zero disables this option.

Reimplemented from Integrator.

Definition at line 200 of file CVodesIntegrator.cpp.

◆ maxSteps()

int maxSteps ( )

overridevirtual

Returns the maximum number of time-steps the integrator can take before reaching the next output time.

Reimplemented from Integrator.

Definition at line 208 of file CVodesIntegrator.cpp.

◆ setMaxErrTestFails()

void setMaxErrTestFails ( int n )

overridevirtual

Set the maximum permissible number of error test failures.

Reimplemented from Integrator.

Definition at line 213 of file CVodesIntegrator.cpp.

◆ solverStats()

AnyMap solverStats ( ) const

overridevirtual

Get solver stats from integrator.

Reimplemented from Integrator.

Definition at line 574 of file CVodesIntegrator.cpp.

◆ setLinearSolverType()

void setLinearSolverType ( const string & linSolverType )

inlineoverridevirtual

Set the linear solver type.

Parameters

linSolverType Type of the linear solver

Reimplemented from Integrator.

Definition at line 60 of file CVodesIntegrator.h.

◆ linearSolverType()

string linearSolverType ( ) const

inlineoverridevirtual

Return the integrator problem type.

Reimplemented from Integrator.

Definition at line 63 of file CVodesIntegrator.h.

◆ setBandwidth()

void setBandwidth	(	int	N_Upper,
		int	N_Lower
	)

inlineoverridevirtual

Reimplemented from Integrator.

Definition at line 66 of file CVodesIntegrator.h.

◆ nSensParams()

int nSensParams ( )

inlineoverridevirtual

Reimplemented from Integrator.

Definition at line 70 of file CVodesIntegrator.h.

◆ sensitivity()

double sensitivity	(	size_t	k,
		size_t	p
	)

overridevirtual

Reimplemented from Integrator.

Definition at line 633 of file CVodesIntegrator.cpp.

◆ setProblemType()

void setProblemType ( int probtype )

overridevirtual

Set the problem type.

Parameters

probtype Type of the problem

Deprecated:: This function is to be removed along with the integer constants used in conditionals to set the problem type currently. This includes DENSE, JAC, NOJAC, BAND, and DIAG

Reimplemented from Integrator.

Definition at line 155 of file CVodesIntegrator.cpp.

◆ getErrorInfo()

string getErrorInfo ( int N )

Returns a string listing the weighted error estimates associated with each solution component.

This information can be used to identify which variables are responsible for integrator failures or unexpected small timesteps.

Definition at line 656 of file CVodesIntegrator.cpp.

◆ applyOptions()

void applyOptions ( )

protected

Applies user-specified options to the underlying CVODES solver.

Called during integrator initialization or reinitialization.

Definition at line 352 of file CVodesIntegrator.cpp.

◆ sensInit()

void sensInit	(	double	t0,
		FuncEval &	func
	)

private

Definition at line 221 of file CVodesIntegrator.cpp.

◆ checkError()

void checkError	(	long	flag,
		const string &	ctMethod,
		const string &	cvodesMethod
	)		const

private

Check whether a CVODES method indicated an error.

If so, throw an exception containing the method name and the error code stashed by the cvodes_err() function.

Definition at line 681 of file CVodesIntegrator.cpp.

Member Data Documentation

◆ m_error_message

string m_error_message

Error message information provide by CVodes.

Definition at line 83 of file CVodesIntegrator.h.

◆ m_neq

size_t m_neq = 0

private

Definition at line 97 of file CVodesIntegrator.h.

◆ m_cvode_mem

void* m_cvode_mem = nullptr

private

Definition at line 98 of file CVodesIntegrator.h.

◆ m_sundials_ctx

SundialsContext m_sundials_ctx

private

SUNContext object for Sundials>=6.0.

Definition at line 99 of file CVodesIntegrator.h.

◆ m_linsol

void* m_linsol = nullptr

private

Sundials linear solver object.

Definition at line 100 of file CVodesIntegrator.h.

◆ m_linsol_matrix

void* m_linsol_matrix = nullptr

private

matrix used by Sundials

Definition at line 101 of file CVodesIntegrator.h.

◆ m_func

FuncEval* m_func = nullptr

private

Definition at line 102 of file CVodesIntegrator.h.

◆ m_t0

double m_t0 = 0.0

private

Definition at line 103 of file CVodesIntegrator.h.

◆ m_time

double m_time

private

The current system time, corresponding to m_y.

Definition at line 106 of file CVodesIntegrator.h.

◆ m_tInteg

double m_tInteg

private

The latest time reached by the integrator. May be greater than m_time.

Definition at line 109 of file CVodesIntegrator.h.

◆ m_y

N_Vector m_y = nullptr

private

The system state at m_time.

Definition at line 112 of file CVodesIntegrator.h.

◆ m_abstol

N_Vector m_abstol = nullptr

private

Definition at line 114 of file CVodesIntegrator.h.

◆ m_dky

N_Vector m_dky = nullptr

private

Definition at line 115 of file CVodesIntegrator.h.

◆ m_type

string m_type = "DENSE"

private

Definition at line 116 of file CVodesIntegrator.h.

◆ m_itol

int m_itol

private

Definition at line 117 of file CVodesIntegrator.h.

◆ m_method

int m_method

private

Definition at line 118 of file CVodesIntegrator.h.

◆ m_maxord

int m_maxord = 0

private

Definition at line 119 of file CVodesIntegrator.h.

◆ m_reltol

double m_reltol = 1e-9

private

Definition at line 120 of file CVodesIntegrator.h.

◆ m_abstols

double m_abstols = 1e-15

private

Definition at line 121 of file CVodesIntegrator.h.

◆ m_reltolsens

double m_reltolsens = 1e-5

private

Definition at line 122 of file CVodesIntegrator.h.

◆ m_abstolsens

double m_abstolsens = 1e-4

private

Definition at line 123 of file CVodesIntegrator.h.

◆ m_nabs

size_t m_nabs = 0

private

Definition at line 124 of file CVodesIntegrator.h.

◆ m_hmax

double m_hmax = 0.0

private

Definition at line 125 of file CVodesIntegrator.h.

◆ m_hmin

double m_hmin = 0.0

private

Definition at line 126 of file CVodesIntegrator.h.

◆ m_maxsteps

int m_maxsteps = 20000

private

Definition at line 127 of file CVodesIntegrator.h.

◆ m_maxErrTestFails

int m_maxErrTestFails = 0

private

Definition at line 128 of file CVodesIntegrator.h.

◆ m_yS

N_Vector* m_yS = nullptr

private

Definition at line 129 of file CVodesIntegrator.h.

◆ m_np

size_t m_np = 0

private

Definition at line 130 of file CVodesIntegrator.h.

◆ m_mupper

int m_mupper = 0

private

Definition at line 131 of file CVodesIntegrator.h.

◆ m_mlower

int m_mlower = 0

private

Definition at line 132 of file CVodesIntegrator.h.

◆ m_sens_ok

bool m_sens_ok = false

private

Indicates whether the sensitivities stored in m_yS have been updated for at the current integrator time.

Definition at line 135 of file CVodesIntegrator.h.

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

Detailed Description

Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CVodesIntegrator()

◆ ~CVodesIntegrator()

Member Function Documentation

◆ setTolerances() [1/2]

◆ setTolerances() [2/2]

◆ setSensitivityTolerances()

◆ initialize()

◆ reinitialize()

◆ integrate()

◆ step()

◆ solution() [1/2]

◆ solution() [2/2]

◆ derivative()

◆ lastOrder()

◆ nEquations()

◆ nEvals()

◆ setMaxOrder()

◆ setMethod()

◆ setMaxStepSize()

◆ setMinStepSize()

◆ setMaxSteps()

◆ maxSteps()

◆ setMaxErrTestFails()

◆ solverStats()

◆ setLinearSolverType()

◆ linearSolverType()

◆ setBandwidth()

◆ nSensParams()

◆ sensitivity()

◆ setProblemType()

◆ getErrorInfo()

◆ applyOptions()

◆ sensInit()

◆ checkError()

Member Data Documentation

◆ m_error_message

◆ m_neq

◆ m_cvode_mem

◆ m_sundials_ctx

◆ m_linsol

◆ m_linsol_matrix

◆ m_func

◆ m_t0

◆ m_time

◆ m_tInteg

◆ m_y

◆ m_abstol

◆ m_dky

◆ m_type

◆ m_itol

◆ m_method

◆ m_maxord

◆ m_reltol

◆ m_abstols

◆ m_reltolsens

◆ m_abstolsens

◆ m_nabs

◆ m_hmax

◆ m_hmin

◆ m_maxsteps

◆ m_maxErrTestFails

◆ m_yS

◆ m_np

◆ m_mupper

◆ m_mlower

◆ m_sens_ok