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Integrator Settings
[Numerical Analysis]

Collaboration diagram for Integrator Settings:

This module contains all functions to set integration options in integratorSettings. More...

Functions

SBML_ODESOLVER_API cvodeSettings_t * CvodeSettings_create ()
 Creates a settings structure with default values.
SBML_ODESOLVER_API cvodeSettings_t * CvodeSettings_createWithTime (double Time, int PrintStep)
 Creates a settings structure with default Values for Errors, MxStep and Swicthes.
SBML_ODESOLVER_API void CvodeSettings_dump (cvodeSettings_t *set)
 Print all cvodeSettings.
SBML_ODESOLVER_API cvodeSettings_t * CvodeSettings_createWith (double Time, int PrintStep, double Error, double RError, int Mxstep, int UseJacobian, int Indefinitely, int HaltOnEvent, int SteadyState, int StoreResults, int Sensitivity, int SensMethod)
 Creates a settings structure from input values.
SBML_ODESOLVER_API cvodeSettings_t * CvodeSettings_clone (cvodeSettings_t *set)
 Creates a settings structure and copies all values from input.
SBML_ODESOLVER_API void CvodeSettings_setErrors (cvodeSettings_t *set, double Error, double RError, int Mxstep)
 Sets absolute and relative error tolerances and maximum number of internal steps during CVODE integration.
SBML_ODESOLVER_API void CvodeSettings_setError (cvodeSettings_t *set, double Error)
 Sets absolute error tolerance.
SBML_ODESOLVER_API void CvodeSettings_setRError (cvodeSettings_t *set, double RError)
 Sets relative error tolerance.
SBML_ODESOLVER_API void CvodeSettings_setMxstep (cvodeSettings_t *set, int Mxstep)
 Sets maximum number of internal steps during CVODE integration.
SBML_ODESOLVER_API void CvodeSettings_setMethod (cvodeSettings_t *set, int CvodeMethod, int MaxOrder)
 Set method non-linear solver methods, and its maximum order (currently the latter cannot really be set, but default to 5 for BDF or 12 for Adams-Moulton!!
SBML_ODESOLVER_API void CvodeSettings_setIterMethod (cvodeSettings_t *set, int i)
 Set method for CVODE integration.
SBML_ODESOLVER_API void CvodeSettings_setMaxOrder (cvodeSettings_t *set, int MaxOrder)
 Sets maximum order of BDF or Adams-Moulton method, respectively, currently this settings is not really used but defaults to 5 for BDF and 12 for Adams-Moulton: ASAP!
SBML_ODESOLVER_API void CvodeSettings_setSwitches (cvodeSettings_t *set, int UseJacobian, int Indefinitely, int HaltOnEvent, int SteadyState, int StoreResults, int Sensitivity, int SensMethod)
 Sets integration switches in cvodeSettings.
SBML_ODESOLVER_API int CvodeSettings_setTime (cvodeSettings_t *set, double EndTime, int PrintStep)
 Calculates a time point series from Endtime and Printstep and sets the time series in cvodeSettings.
SBML_ODESOLVER_API int CvodeSettings_setTimeStep (cvodeSettings_t *set, int i, double time)
 Sets the ith time step for the integration, where 0 < i <= PrintStep.
SBML_ODESOLVER_API void CvodeSettings_setJacobian (cvodeSettings_t *set, int i)
 Sets use of generated Jacobian matrix (i=1) or of CVODE's internal approximation (i=0).
SBML_ODESOLVER_API void CvodeSettings_setIndefinitely (cvodeSettings_t *set, int i)
 Sets indefinite integration (i=1).
SBML_ODESOLVER_API void CvodeSettings_setHaltOnEvent (cvodeSettings_t *set, int i)
 Sets event handling, stop (1, default) or don't stop (0) on events.
SBML_ODESOLVER_API void CvodeSettings_setSteadyState (cvodeSettings_t *set, int i)
 Sets steady state handling: if i==1, the integration will stop upon an approximate detection of a steady state, which is here defined as some threshold value of the mean value and standard deviation of current ODE values.
SBML_ODESOLVER_API void CvodeSettings_setStoreResults (cvodeSettings_t *set, int i)
 Results will only be stored, if i==1 and if a finite integration has been chosen (CvodeSettings_setIndefinitely(settings, 0)).
SBML_ODESOLVER_API void CvodeSettings_setSensitivity (cvodeSettings_t *set, int i)
 Activate sensitivity analysis with 1; also sets to default sensitivity method `simultaneous' (setSensMethod(set, 0);.
SBML_ODESOLVER_API void CvodeSettings_setSensMethod (cvodeSettings_t *set, int i)
 Set method for sensitivity analysis: 0: simultaneous 1: staggered, 2: staggered1.
SBML_ODESOLVER_API double CvodeSettings_getEndTime (cvodeSettings_t *set)
 Returns the last time point of integration or -1, if Indefinitely is set to TRUE (1);.
SBML_ODESOLVER_API double CvodeSettings_getTimeStep (cvodeSettings_t *set)
 Returns the time step of integration; if infinite integration has been chosen, this is only the first time step.
SBML_ODESOLVER_API int CvodeSettings_getPrintsteps (cvodeSettings_t *set)
 Returns the number of integration steps or -1, if infinite integration has been chosen.
SBML_ODESOLVER_API double CvodeSettings_getTime (cvodeSettings_t *set, int i)
 Returns the time of the ith time step, where 0 <= i < PrintStep, unless infinite integration has been chosen.
SBML_ODESOLVER_API double CvodeSettings_getError (cvodeSettings_t *set)
 Returns the absolute error tolerance.
SBML_ODESOLVER_API double CvodeSettings_getRError (cvodeSettings_t *set)
 Returns the relative error tolerance.
SBML_ODESOLVER_API int CvodeSettings_getMxstep (cvodeSettings_t *set)
 Returns the maximum number of internal time steps taken by CVODE to reach the next output time (printstep).
SBML_ODESOLVER_API char * CvodeSettings_getMethod (cvodeSettings_t *set)
 Get non-linear solver method (BDF or ADAMS-MOULTON).
SBML_ODESOLVER_API int CvodeSettings_getMaxOrder (cvodeSettings_t *set)
 Get maximum order of non-linear solver method.
SBML_ODESOLVER_API char * CvodeSettings_getIterMethod (cvodeSettings_t *set)
 Get non-linear solver iteration type (NEWTON or FUNCTIONAL).
SBML_ODESOLVER_API int CvodeSettings_getJacobian (cvodeSettings_t *set)
 Returns 1, if the automatically generated or 0 if CVODE's internal approximation of the jacobian matrix will be used by CVODE.
SBML_ODESOLVER_API int CvodeSettings_getIndefinitely (cvodeSettings_t *set)
 Returns 1, if infinite integration has been chosen, and 0 otherwise.
SBML_ODESOLVER_API int CvodeSettings_getHaltOnEvent (cvodeSettings_t *set)
 Returns 1, if integration should stop upon an event trigger and 0 if integration should continue after evaluation of event assignments.
SBML_ODESOLVER_API int CvodeSettings_getSteadyState (cvodeSettings_t *set)
 Returns 1, if integration should stop upon detection of a steady state, and 0 if integration should continue.
SBML_ODESOLVER_API int CvodeSettings_getStoreResults (cvodeSettings_t *set)
 Returns 1, if integration results should be stored internally, and 0 if not.
SBML_ODESOLVER_API int CvodeSettings_getSensitivity (cvodeSettings_t *set)
 Returns 1, if sensitivity analysis is requested and CVODES will be used.
SBML_ODESOLVER_API char * CvodeSettings_getSensMethod (cvodeSettings_t *set)
 Get sensitivity method `simultaneous', `staggered' or `staggered1'.
SBML_ODESOLVER_API void CvodeSettings_free (cvodeSettings_t *set)
 Frees cvodeSettings.

Detailed Description

This module contains all functions to set integration options in integratorSettings.

With these functions an application can choose integration time, methods and options like error tolerances.

Function Documentation

SBML_ODESOLVER_API cvodeSettings_t* CvodeSettings_create (   ) 
 

Creates a settings structure with default values.

DEFAULT INTEGRATION SETTINGS ARE

1) CVODE SPECIFIC SETTINGS:

absolute error tolerance for each output time: 1e-18

relative error tolerance for each output time: 1e-10

max. nr. of steps to reach next output time: 10000

Nonlinear solver method: 0: BDF

Maximum Order: 5

Iteration method: 0: NEWTON

Sensitivity: 0: no

method: 0: simultaneous

2) SOSlib SPECIFIC SETTINGS:

Jacobian matrix: 1: generate Jacobian

Indefinitely: 0: finite integration

Event Handling: 0: keep integrating

Steady States: 0: keep integrating

Store Results: 1: store results (only for finite integration)

3) TIME SETTINGS:

endtime: 1

steps: 10

SBML_ODESOLVER_API cvodeSettings_t* CvodeSettings_createWithTime (  double  Time,
int  PrintStep
) 
 

Creates a settings structure with default Values for Errors, MxStep and Swicthes.

SBML_ODESOLVER_API void CvodeSettings_dump (  cvodeSettings_t *  set  ) 
 

Print all cvodeSettings.

SBML_ODESOLVER_API cvodeSettings_t* CvodeSettings_createWith (  double  Time,
int  PrintStep,
double  Error,
double  RError,
int  Mxstep,
int  UseJacobian,
int  Indefinitely,
int  HaltOnEvent,
int  SteadyState,
int  StoreResults,
int  Sensitivity,
int  SensMethod
) 
 

Creates a settings structure from input values.

WARNING: this function's type signature will change with time, as new settings will be required for other solvers!

SBML_ODESOLVER_API cvodeSettings_t* CvodeSettings_clone (  cvodeSettings_t *  set  ) 
 

Creates a settings structure and copies all values from input.

SBML_ODESOLVER_API void CvodeSettings_setErrors (  cvodeSettings_t *  set,
double  Error,
double  RError,
int  Mxstep
) 
 

Sets absolute and relative error tolerances and maximum number of internal steps during CVODE integration.

SBML_ODESOLVER_API void CvodeSettings_setError (  cvodeSettings_t *  set,
double  Error
) 
 

Sets absolute error tolerance.

SBML_ODESOLVER_API void CvodeSettings_setRError (  cvodeSettings_t *  set,
double  RError
) 
 

Sets relative error tolerance.

SBML_ODESOLVER_API void CvodeSettings_setMxstep (  cvodeSettings_t *  set,
int  Mxstep
) 
 

Sets maximum number of internal steps during CVODE integration.

SBML_ODESOLVER_API void CvodeSettings_setMethod (  cvodeSettings_t *  set,
int  CvodeMethod,
int  MaxOrder
) 
 

Set method non-linear solver methods, and its maximum order (currently the latter cannot really be set, but default to 5 for BDF or 12 for Adams-Moulton!!

CvodeMethod: 0: BDF (default); 1: Adams-Moulton,
MaxOrder: maximum order (default: 5 for BDF, 12 for Adams-Moulton.

SBML_ODESOLVER_API void CvodeSettings_setIterMethod (  cvodeSettings_t *  set,
int  i
) 
 

Set method for CVODE integration.

0: NEWTON (default)
1: FUNCTIONAL

SBML_ODESOLVER_API void CvodeSettings_setMaxOrder (  cvodeSettings_t *  set,
int  MaxOrder
) 
 

Sets maximum order of BDF or Adams-Moulton method, respectively, currently this settings is not really used but defaults to 5 for BDF and 12 for Adams-Moulton: ASAP!

SBML_ODESOLVER_API void CvodeSettings_setSwitches (  cvodeSettings_t *  set,
int  UseJacobian,
int  Indefinitely,
int  HaltOnEvent,
int  SteadyState,
int  StoreResults,
int  Sensitivity,
int  SensMethod
) 
 

Sets integration switches in cvodeSettings.

WARNING: this function's type signature will change with time, as new settings will be required for other solvers!

SBML_ODESOLVER_API int CvodeSettings_setTime (  cvodeSettings_t *  set,
double  EndTime,
int  PrintStep
) 
 

Calculates a time point series from Endtime and Printstep and sets the time series in cvodeSettings.

Returns 1, if sucessful and 0, if not.

SBML_ODESOLVER_API int CvodeSettings_setTimeStep (  cvodeSettings_t *  set,
int  i,
double  time
) 
 

Sets the ith time step for the integration, where 0 < i <= PrintStep.

Returns 1, if sucessful and 0, if not.
The first time is always 0 and can not be set at the moment, as an SBML input file is supposed to start with 0.

SBML_ODESOLVER_API void CvodeSettings_setJacobian (  cvodeSettings_t *  set,
int  i
) 
 

Sets use of generated Jacobian matrix (i=1) or of CVODE's internal approximation (i=0).

If construction of the Jacobian matrix fails, the internal approximation will be used in any case!

SBML_ODESOLVER_API void CvodeSettings_setIndefinitely (  cvodeSettings_t *  set,
int  i
) 
 

Sets indefinite integration (i=1).

For indefinite integration Time will be used as integration step and PrintStep will be ignored.

SBML_ODESOLVER_API void CvodeSettings_setHaltOnEvent (  cvodeSettings_t *  set,
int  i
) 
 

Sets event handling, stop (1, default) or don't stop (0) on events.

If i==1, the integration will stop upon detection of an event and evaluation of event assignments.

If i==0 the integration continues after evaluation of event assignments. CAUTION: the accuracy of event evaluations depends on the chosen printstep values!

SBML_ODESOLVER_API void CvodeSettings_setSteadyState (  cvodeSettings_t *  set,
int  i
) 
 

Sets steady state handling: if i==1, the integration will stop upon an approximate detection of a steady state, which is here defined as some threshold value of the mean value and standard deviation of current ODE values.

SBML_ODESOLVER_API void CvodeSettings_setStoreResults (  cvodeSettings_t *  set,
int  i
) 
 

Results will only be stored, if i==1 and if a finite integration has been chosen (CvodeSettings_setIndefinitely(settings, 0)).

The results can be retrieved after integration has been finished. If i==0 or infinite integration has been chosen, results can only be retrieved during integration via variableIndex interface or dump functions for the integratorInstance.

SBML_ODESOLVER_API void CvodeSettings_setSensitivity (  cvodeSettings_t *  set,
int  i
) 
 

Activate sensitivity analysis with 1; also sets to default sensitivity method `simultaneous' (setSensMethod(set, 0);.

SBML_ODESOLVER_API void CvodeSettings_setSensMethod (  cvodeSettings_t *  set,
int  i
) 
 

Set method for sensitivity analysis: 0: simultaneous 1: staggered, 2: staggered1.

SBML_ODESOLVER_API double CvodeSettings_getEndTime (  cvodeSettings_t *  set  ) 
 

Returns the last time point of integration or -1, if Indefinitely is set to TRUE (1);.

SBML_ODESOLVER_API double CvodeSettings_getTimeStep (  cvodeSettings_t *  set  ) 
 

Returns the time step of integration; if infinite integration has been chosen, this is only the first time step.

SBML_ODESOLVER_API int CvodeSettings_getPrintsteps (  cvodeSettings_t *  set  ) 
 

Returns the number of integration steps or -1, if infinite integration has been chosen.

SBML_ODESOLVER_API double CvodeSettings_getTime (  cvodeSettings_t *  set,
int  i
) 
 

Returns the time of the ith time step, where 0 <= i < PrintStep, unless infinite integration has been chosen.

SBML_ODESOLVER_API double CvodeSettings_getError (  cvodeSettings_t *  set  ) 
 

Returns the absolute error tolerance.

SBML_ODESOLVER_API double CvodeSettings_getRError (  cvodeSettings_t *  set  ) 
 

Returns the relative error tolerance.

SBML_ODESOLVER_API int CvodeSettings_getMxstep (  cvodeSettings_t *  set  ) 
 

Returns the maximum number of internal time steps taken by CVODE to reach the next output time (printstep).

SBML_ODESOLVER_API char* CvodeSettings_getMethod (  cvodeSettings_t *  set  ) 
 

Get non-linear solver method (BDF or ADAMS-MOULTON).

SBML_ODESOLVER_API int CvodeSettings_getMaxOrder (  cvodeSettings_t *  set  ) 
 

Get maximum order of non-linear solver method.

SBML_ODESOLVER_API char* CvodeSettings_getIterMethod (  cvodeSettings_t *  set  ) 
 

Get non-linear solver iteration type (NEWTON or FUNCTIONAL).

SBML_ODESOLVER_API int CvodeSettings_getJacobian (  cvodeSettings_t *  set  ) 
 

Returns 1, if the automatically generated or 0 if CVODE's internal approximation of the jacobian matrix will be used by CVODE.

SBML_ODESOLVER_API int CvodeSettings_getIndefinitely (  cvodeSettings_t *  set  ) 
 

Returns 1, if infinite integration has been chosen, and 0 otherwise.

SBML_ODESOLVER_API int CvodeSettings_getHaltOnEvent (  cvodeSettings_t *  set  ) 
 

Returns 1, if integration should stop upon an event trigger and 0 if integration should continue after evaluation of event assignments.

SBML_ODESOLVER_API int CvodeSettings_getSteadyState (  cvodeSettings_t *  set  ) 
 

Returns 1, if integration should stop upon detection of a steady state, and 0 if integration should continue.

SBML_ODESOLVER_API int CvodeSettings_getStoreResults (  cvodeSettings_t *  set  ) 
 

Returns 1, if integration results should be stored internally, and 0 if not.

If set to 0 current values can be retrieved during an integration loop, and the values at the end time of integration afterwards.

SBML_ODESOLVER_API int CvodeSettings_getSensitivity (  cvodeSettings_t *  set  ) 
 

Returns 1, if sensitivity analysis is requested and CVODES will be used.

SBML_ODESOLVER_API char* CvodeSettings_getSensMethod (  cvodeSettings_t *  set  ) 
 

Get sensitivity method `simultaneous', `staggered' or `staggered1'.

SBML_ODESOLVER_API void CvodeSettings_free (  cvodeSettings_t *  set  ) 
 

Frees cvodeSettings.

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