int
main (int argc, char *argv[]){
int i, j;
char *model, *parameter, *reaction;
double start, end, steps, value;
double time ;
double printstep;
/* libSBML types */
SBMLDocument_t *d;
SBMLReader_t *sr;
/* SOSlib types */
cvodeSettings_t *set;
varySettings_t *vs;
SBMLResultsMatrix_t *resM;
SBMLResults_t *results;
/* parsing command-line arguments */
if (argc < 8 ) {
fprintf(stderr,
"usage %s sbml-model-file simulation-time time-steps"
" start-value end-value step-number parameter-id"
" [optional reaction-id]\n",
argv[0]);
exit(EXIT_FAILURE);
}
model = argv[1];
time = atof(argv[2]);
printstep = atoi(argv[3]);
parameter = argv[7];
start = atof(argv[4]);
end = atof(argv[5]);
steps = atoi(argv[6]);
if ( argc > 8 ) {
reaction = argv[8];
}
else{
reaction = NULL;
}
printf("### Varying parameter %s (reaction %s) from %f to %f in %f steps\n",
parameter, reaction, start, end, steps);
/* parsing the SBML model with libSBML */
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, model);
SBMLReader_free(sr);
/* Setting SBML ODE Solver integration parameters with default values */
set = CvodeSettings_create();
/* resetting the values we need */
CvodeSettings_setTime(set, time, printstep);
CvodeSettings_setErrors(set, 1e-18, 1e-10, 10000);
CvodeSettings_setSwitches(set, 1, 0, 1, 1, 1, 0, 0);
CvodeSettings_setSteadyState(set, 1);
/* Setting SBML Ode Solver batch integration parameters */
vs = VarySettings_allocate(1, steps+1);
VarySettings_addParameter(vs, parameter, reaction, start, end);
VarySettings_dump(vs);
/* calling the SBML ODE Solver Batch function,
and retrieving SBMLResults */
resM = SBML_odeSolverBatch(d, set, vs);
if ( resM == NULL ) {
printf("### Parameter variation not succesful!\n");
return(0);
}
/* we don't need these anymore */
CvodeSettings_free(set);
SBMLDocument_free(d);
VarySettings_free(vs);
results = resM->results[0][0];
for ( i=0; i<resM->i; i++ ) {
for ( j=0; j<resM->j; j++ ) {
results = SBMLResultsMatrix_getResults(resM, i, j);
printf("### RESULTS Parameter %d, Step %d \n", i+1, j+1);
/* printing results only for species*/
SBMLResults_dumpSpecies(results);
}
}
/* SolverError_dumpAndClearErrors(); */
SBMLResultsMatrix_free(resM);
return (EXIT_SUCCESS);
}
int
main (int argc, char *argv[]){
int i;
char *model;
/* libSBML types */
SBMLDocument_t *d;
SBMLReader_t *sr;
/* SOSlib types */
SBMLResults_t *results;
cvodeSettings_t *set;
double printstep;
double endtime;
/* parsing command-line arguments */
if (argc < 2 ) {
fprintf(stderr,
"usage %s sbml-model-file\n",
argv[0]);
exit(EXIT_FAILURE);
}
model = argv[1];
/* parsing the SBML model with libSBML */
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, model);
SBMLReader_free(sr);
/* Setting SBML ODE Solver integration parameters */
set = CvodeSettings_create();
/* setting endtime to 25 and printstep number to 6 */
printstep = 6;
endtime = 25;
CvodeSettings_setTime(set, endtime, printstep);
/* writing predefined output times:
IMPORTANT: can not exceed the set printstep number !!
and first time must equal 0 !! */
CvodeSettings_setTimeStep(set, 1, 0.5);
for ( i=2; i<=CvodeSettings_getPrintsteps(set); i++ )
CvodeSettings_setTimeStep(set, i, (i-1)*(i-1));
/* printing integration settings */
/* CvodeSettings_dump(set); */
/* calling the SBML ODE Solver, and retrieving SBMLResults */
results = SBML_odeSolver(d, set);
CvodeSettings_free(set);
SBMLDocument_free(d);
if ( results == NULL ) {
printf("Integration not sucessful!\n");
return (EXIT_FAILURE);
}
/* printing results only for species*/
SBMLResults_dumpSpecies(results);
/* now we can also free the result structure */
SBMLResults_free(results);
return (EXIT_SUCCESS);
}
