CVODES ODE Solver: x(t)
[ODE/DAE Integrator Interface]

Collaboration diagram for CVODES ODE Solver: x(t):

This module contains the functions that call SUNDIALS CVODES solver routines for stiff and non-stiff ODE systems. More...

Modules
	CVODES Forward Sensitivity: dx(t)/dp
	This module contains the functions that set up and call SUNDIALS CVODES forward sensitivity analysis routines.
Functions
SBML_ODESOLVER_API int	IntegratorInstance_cvodeOneStep (integratorInstance_t *engine)
	Calls CVODE to move the current simulation one time step.
int	IntegratorInstance_createCVODESolverStructures (integratorInstance_t *engine)
	creates CVODE structures and fills cvodeSolver, returns 1 on success or 0 on failure
void	IntegratorInstance_freeCVODESolverStructures (integratorInstance_t *engine)
SBML_ODESOLVER_API void	IntegratorInstance_printCVODEStatistics (integratorInstance_t *engine, FILE *f)
	Prints some final statistics of the calls to CVODE routines, that are located in CVODE's iopt array.
int	check_flag (void *flagvalue, char *funcname, int opt, FILE *f)
void	f (realtype t, N_Vector y, N_Vector ydot, void *f_data)
	f routine: Compute f(t,x) = df/dx .
void	JacODE (long int N, DenseMat J, realtype t, N_Vector y, N_Vector fy, void *jac_data, N_Vector vtemp1, N_Vector vtemp2, N_Vector vtemp3)
	Jacobian routine: Compute J(t,x) = df/dx.

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Detailed Description

This module contains the functions that call SUNDIALS CVODES solver routines for stiff and non-stiff ODE systems.

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Function Documentation

SBML_ODESOLVER_API int IntegratorInstance_cvodeOneStep (  integratorInstance_t *  engine  )

Calls CVODE to move the current simulation one time step. produces appropriate error messages on failures and returns 1 if the integration can continue, 0 otherwise. This function is called by IntegratorInstance_integrateOneStep, but could also be called directly by a calling application that is sure to use CVODES (and not e.g. IDA), to avoid the if statements in the wrapper function.

int IntegratorInstance_createCVODESolverStructures (  integratorInstance_t *  engine  )

creates CVODE structures and fills cvodeSolver, returns 1 on success or 0 on failure !! should use simplified ASTs for construction !!! Allocate y, abstol vectors Initialize y, abstol vectors Call CVodeCreate to create the non-linear solver memory: Nonlinear Solver: CV_BDF Backward Differentiation Formula method CV_ADAMS Adams-Moulton method Iteration Method: CV_NEWTON Newton iteration method CV_FUNCTIONAL functional iteration method !! max. order should be set here !! Call CVodeMalloc to initialize the integrator memory: cvode_mem: pointer to the CVode memory block returned by CVodeCreate f: user's right hand side function in f(x,p,t) = dx/dt t0: initial value of time y: the initial dependent variable vector (called in x in the docu) CV_SV: specifies scalar relative and vector absolute tolerances reltol: the scalar relative tolerance abstol: pointer to the absolute tolerance vector Link the main integrator with data for right-hand side function Link the main integrator with the CVDENSE linear solver Set the routine used by the CVDENSE linear solver to approximate the Jacobian matrix to ... Set maximum number of internal steps to be taken by the solver in its attempt to reach tout !! will need adaptation to selected sens.analysis !!!

void IntegratorInstance_freeCVODESolverStructures (  integratorInstance_t *  engine  )

SBML_ODESOLVER_API void IntegratorInstance_printCVODEStatistics (  integratorInstance_t *  engine, FILE *  f )

Prints some final statistics of the calls to CVODE routines, that are located in CVODE's iopt array.

static int check_flag (  void *  flagvalue, char *  funcname, int  opt, FILE *  f )

void f (  realtype  t, N_Vector  y, N_Vector  ydot, void *  f_data )

f routine: Compute f(t,x) = df/dx . This function is called by CVODE's integration routines every time required. It evaluates the ODEs with the current variable values, as supplied by CVODE's N_Vector y vector containing the values of all variables (called x in this documentation. These values are first written back to CvodeData. Then every ODE is passed to evaluateAST, together with the cvodeData_t *, and this function calculates the current value of the ODE. The returned value is written back to CVODE's N_Vector(ydot) vector that contains the values of the ODEs. update parameters: p is modified by CVODES, if fS could not be generated update ODE variables from CVODE update assignment rules evaluate ODEs f(x,p,t) = dx/dt

void JacODE (  long int  N, DenseMat  J, realtype  t, N_Vector  y, N_Vector  fy, void *  jac_data, N_Vector  vtemp1, N_Vector  vtemp2, N_Vector  vtemp3 )

Jacobian routine: Compute J(t,x) = df/dx. This function is (optionally) called by CVODE's integration routines every time required. Very similar to the f routine, it evaluates the Jacobian matrix equations with CVODE's current values and writes the results back to CVODE's internal vector DENSE_ELEM(J,i,j). update parameters: p is modified by CVODES, if fS could not be generated update ODE variables from CVODE update assignment rules update time evaluate Jacobian J = df/dx

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