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. More...

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

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

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

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

void	reinitialize (double t0, FuncEval &func) override

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

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

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

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

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

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

int	nEquations () const override
	The number of equations. More...

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

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

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

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

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

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

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

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

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

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

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

void	setBandwidth (int N_Upper, int N_Lower) override

int	nSensParams () override

double	sensitivity (size_t k, size_t p) override

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

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

virtual	~Integrator ()
	Destructor. More...

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

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

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

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

virtual int	maxOrder () const

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. More...

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

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. More...

Private Attributes
size_t	m_neq = 0

void *	m_cvode_mem = nullptr

SundialsContext	m_sundials_ctx
	SUNContext object for Sundials>=6.0. More...

void *	m_linsol = nullptr
	Sundials linear solver object. More...

void *	m_linsol_matrix = nullptr
	matrix used by Sundials More...

FuncEval *	m_func = nullptr

double	m_t0 = 0.0

double	m_time
	The current system time, corresponding to m_y. More...

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

N_Vector	m_y = nullptr
	The system state at m_time. More...

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. More...

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() More...

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

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.

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 233 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 477 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 515 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 535 of file CVodesIntegrator.cpp.

◆ lastOrder()

int lastOrder ( ) const

overridevirtual

Order used during the last solution step.

Reimplemented from Integrator.

Definition at line 542 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 549 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 155 of file CVodesIntegrator.cpp.

◆ setMaxStepSize()

void setMaxStepSize ( double hmax )

overridevirtual

Set the maximum step size.

Reimplemented from Integrator.

Definition at line 166 of file CVodesIntegrator.cpp.

◆ setMinStepSize()

void setMinStepSize ( double hmin )

overridevirtual

Set the minimum step size.

Reimplemented from Integrator.

Definition at line 174 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 182 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 190 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 195 of file CVodesIntegrator.cpp.

◆ solverStats()

AnyMap solverStats ( ) const

overridevirtual

Get solver stats from integrator.

Reimplemented from Integrator.

Definition at line 556 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.

◆ 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 638 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 334 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 663 of file CVodesIntegrator.cpp.

Member Data Documentation

◆ m_error_message

string m_error_message

Error message information provide by CVodes.

Definition at line 82 of file CVodesIntegrator.h.

◆ m_sundials_ctx

SundialsContext m_sundials_ctx

private

SUNContext object for Sundials>=6.0.

Definition at line 98 of file CVodesIntegrator.h.

◆ m_linsol

void* m_linsol = nullptr

private

Sundials linear solver object.

Definition at line 99 of file CVodesIntegrator.h.

◆ m_linsol_matrix

void* m_linsol_matrix = nullptr

private

matrix used by Sundials

Definition at line 100 of file CVodesIntegrator.h.

◆ m_time

double m_time

private

The current system time, corresponding to m_y.

Definition at line 105 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 108 of file CVodesIntegrator.h.

◆ m_y

N_Vector m_y = nullptr

private

The system state at m_time.

Definition at line 111 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 134 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()

Member Function Documentation

◆ setTolerances() [1/2]

◆ setTolerances() [2/2]

◆ setSensitivityTolerances()

◆ initialize()

◆ integrate()

◆ step()

◆ solution() [1/2]

◆ solution() [2/2]

◆ derivative()

◆ lastOrder()

◆ nEquations()

◆ nEvals()

◆ setMaxOrder()

◆ setMethod()

◆ setMaxStepSize()

◆ setMinStepSize()

◆ setMaxSteps()

◆ maxSteps()

◆ setMaxErrTestFails()

◆ solverStats()

◆ setLinearSolverType()

◆ linearSolverType()

◆ getErrorInfo()

◆ applyOptions()

◆ checkError()

Member Data Documentation

◆ m_error_message

◆ m_sundials_ctx

◆ m_linsol

◆ m_linsol_matrix

◆ m_time

◆ m_tInteg

◆ m_y

◆ m_sens_ok