#include <malloc.h>#include <string.h>#include <math.h>#include <stdio.h>#include <stdlib.h>#include <cvodes.h>#include <kinsol.h>#include <cvdense.h>#include <nvector_serial.h>#include "sbmlsolver/cvodedata.h"#include "sbmlsolver/processAST.h"#include "sbmlsolver/odeModel.h"#include "sbmlsolver/variableIndex.h"#include "sbmlsolver/solverError.h"#include "sbmlsolver/integratorInstance.h"#include "sbmlsolver/cvodeSolver.h"#include "sbmlsolver/sensSolver.h"#include "sbmlsolver/modelSimplify.h"Include dependency graph for integratorInstance.c:
Functions | |
| SBML_ODESOLVER_API integratorInstance_t * | IntegratorInstance_create (odeModel_t *om, cvodeSettings_t *opt) |
| Creates an new integratorInstance. | |
| SBML_ODESOLVER_API int | IntegratorInstance_set (integratorInstance_t *engine, cvodeSettings_t *opt) |
| Resets and existing integratorInstance with new settings. | |
| SBML_ODESOLVER_API int | IntegratorInstance_reset (integratorInstance_t *engine) |
| Resets and integratorInstance to its initial values. | |
| SBML_ODESOLVER_API cvodeSettings_t * | IntegratorInstance_getSettings (integratorInstance_t *engine) |
| Returns the settings of this integratorInstance. | |
| SBML_ODESOLVER_API void | IntegratorInstance_copyVariableState (integratorInstance_t *target, integratorInstance_t *source) |
| Copies variable and parameter values between two integratorInstances that have been created from the same odeModel. | |
| SBML_ODESOLVER_API double | IntegratorInstance_getTime (integratorInstance_t *engine) |
| Returns the current time of an integration. | |
| SBML_ODESOLVER_API int | IntegratorInstance_setNextTimeStep (integratorInstance_t *engine, double nexttime) |
| Sets the next output time for infinite integration. | |
| SBML_ODESOLVER_API double | IntegratorInstance_getVariableValue (integratorInstance_t *engine, variableIndex_t *vi) |
| Gets the value of a variable or parameter during an integration via its variableIndex. | |
| SBML_ODESOLVER_API double | IntegratorInstance_getSensitivity (integratorInstance_t *engine, variableIndex_t *y, variableIndex_t *p) |
| Gets the sensitivity of variable y to parameter p at the current time. | |
| SBML_ODESOLVER_API void | IntegratorInstance_dumpNames (integratorInstance_t *engine) |
| Prints variable names, the first value is the time,. | |
| SBML_ODESOLVER_API void | IntegratorInstance_dumpData (integratorInstance_t *engine) |
| Prints the current integration data,. | |
| SBML_ODESOLVER_API void | IntegratorInstance_dumpYSensitivities (integratorInstance_t *engine, variableIndex_t *y) |
| Prints the current time, current value of variable y and sensitivities to all parameters for which calculated. | |
| SBML_ODESOLVER_API void | IntegratorInstance_dumpPSensitivities (integratorInstance_t *engine, variableIndex_t *p) |
| Prints the current time, the value of parameter p and all variable's sensitivities Si to p, where i = 1 to NEQ. | |
| SBML_ODESOLVER_API cvodeData_t * | IntegratorInstance_getData (integratorInstance_t *engine) |
| Returns a pointer cvodeData of the integratorInstance, which contains the current values of all variables. | |
| SBML_ODESOLVER_API int | IntegratorInstance_integrate (integratorInstance_t *engine) |
| Starts the default integration loop with standard error handling and returns 0 if integration was OK, and the error code if not. | |
| SBML_ODESOLVER_API int | IntegratorInstance_timeCourseCompleted (integratorInstance_t *engine) |
| Returns TRUE if the requested timecourse has been completed for the passed integratorInstance. | |
| SBML_ODESOLVER_API cvodeResults_t * | IntegratorInstance_createResults (integratorInstance_t *engine) |
| Creates and returns a cvodeResults structure containing the results of one integration run and NULL if not successful. | |
| SBML_ODESOLVER_API int | IntegratorInstance_updateModel (integratorInstance_t *engine) |
| Writes current simulation data to original model. | |
| SBML_ODESOLVER_API int | IntegratorInstance_simpleOneStep (integratorInstance_t *engine) |
| Handles the simple case of models that contain no ODEs. | |
| int | IntegratorInstance_updateData (integratorInstance_t *engine) |
| Default function for updating data, to be used by solvers after they have calculate x(t) and updated the time. | |
| SBML_ODESOLVER_API int | IntegratorInstance_checkTrigger (integratorInstance_t *engine) |
| Evaluates event trigger expressions and executes event assignments for those triggers that are true. | |
| SBML_ODESOLVER_API int | IntegratorInstance_checkSteadyState (integratorInstance_t *engine) |
| Approximate identification of a steady state. | |
| SBML_ODESOLVER_API void | IntegratorInstance_setVariableValue (integratorInstance_t *engine, variableIndex_t *vi, double value) |
| Sets the value of a variable or parameter during an integration via its variableIndex. | |
| SBML_ODESOLVER_API int | IntegratorInstance_integrateOneStep (integratorInstance_t *engine) |
| Moves the current integration one step forward and switches between different solvers for filling ODE variables. | |
| SBML_ODESOLVER_API void | IntegratorInstance_dumpSolver (integratorInstance_t *engine) |
| Prints the current state of the solver. | |
| SBML_ODESOLVER_API void | IntegratorInstance_free (integratorInstance_t *engine) |
| Frees an integratorInstance, including cvodeData. | |
| SBML_ODESOLVER_API int | IntegratorInstance_handleError (integratorInstance_t *engine) |
| Standard handler for when the integrate function fails. | |
| SBML_ODESOLVER_API void | IntegratorInstance_printStatistics (integratorInstance_t *engine, FILE *f) |
| Prints some final statistics of the solver. | |
1.4.4