static int CvodeData_allocateSens(cvodeData_t *data, int neq, int nsens)
{
int i;
ASSIGN_NEW_MEMORY_BLOCK(data->p, nsens, realtype, 0);
ASSIGN_NEW_MEMORY_BLOCK(data->p_orig, nsens, realtype, 0);
ASSIGN_NEW_MEMORY_BLOCK(data->sensitivity, neq, double *, 0);
for ( i=0; i<neq; i++ )
ASSIGN_NEW_MEMORY_BLOCK(data->sensitivity[i], nsens, double, 0);
data->nsens = nsens;
data->neq = neq;
return 1;
}
/* creates CVODES forward sensitivity solver structures
return 1 => success
return 0 => failure
*/
int
IntegratorInstance_createCVODESSolverStructures(integratorInstance_t *engine)
{
int i, j, flag, neq, ns;
realtype *ydata, *abstoldata, *ySdata, *senstoldata;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeSolver_t *solver = engine->solver;
cvodeSettings_t *opt = engine->opt;
/* realtype pbar[data->nsens+1]; */
/*int *plist; removed by AMF 8/11/05
realtype *pbar;
ASSIGN_NEW_MEMORY_BLOCK(plist, data->nsens+1, int, 0)
ASSIGN_NEW_MEMORY_BLOCK(pbar, data->nsens+1, realtype, 0)*/
/***** adding sensitivity specific structures ******/
/**
* construct sensitivity related structures
*/
/* free sensitivity from former runs (changed for non-default cases!) */
ODEModel_freeSensitivity(om);
/* if jacobian matrix has been constructed successfully,
construct sensitivity matrix dx/dp, sets om->sensitivity
to 1 if successful, 0 otherwise */
/*!!! this function will require additional input for
non-default case, via sensitivity input settings! !!!*/
if ( om->jacobian )
ODEModel_constructSensitivity(om);
else {
om->sensitivity = 0;
om->jacob_sens = NULL;
om->nsens = om->nconst;
ASSIGN_NEW_MEMORY_BLOCK(om->index_sens, om->nsens, int, 0);
/*!!! non-default case:
these values should be passed for other cases !!!*/
for ( i=0; i<om->nsens; i++ )
om->index_sens[i] = om->neq + om->nass + i;
}
engine->solver->nsens = data->nsens;
solver->yS = N_VNewVectorArray_Serial(data->nsens, data->neq);
if (check_flag((void *)solver->yS, "N_VNewVectorArray_Serial",
1, stderr))
return(0);
/*
* (re)initialize ySdata sensitivities
*/
/* absolute tolerance for sensitivity error control */
solver->senstol = N_VNew_Serial(data->nsens);
abstoldata = NV_DATA_S(solver->senstol);
for ( j=0; j<data->nsens; j++ ) {
abstoldata[j] = 1e-4;
ySdata = NV_DATA_S(solver->yS[j]);
for ( i=0; i<data->neq; i++ )
ySdata[i] = data->sensitivity[i][j];
}
/*
* set method
*/
if ( opt->SensMethod == 0 )
flag =CVodeSensMalloc(solver->cvode_mem,data->nsens,
CV_SIMULTANEOUS, solver->yS);
else if ( opt->SensMethod == 1 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED, solver->yS);
else if ( opt->SensMethod == 2 )
flag = CVodeSensMalloc(solver->cvode_mem, data->nsens,
CV_STAGGERED1, solver->yS);
if(check_flag(&flag, "CVodeSensMalloc", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
/* *** set parameter values or R.H.S function fS *****/
/* NOTES: */
/* !!! plist could later be used to specify requested parameters
for sens.analysis !!! */
/* was construction of Jacobian and
parametric matrix successfull ? */
if ( om->sensitivity && om->jacobian ) {
flag = CVodeSetSensRhs1Fn(solver->cvode_mem, fS);
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensFdata(solver->cvode_mem, data);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
data->p = NULL;
}
else {
ASSIGN_NEW_MEMORY_BLOCK(data->p, data->nsens, realtype, 0);
for ( i=0; i<data->nsens; i++ ) {
/* data->p is only required if R.H.S. fS cannot be supplied */
/* plist[i] = i+1; */
data->p[i] = data->value[om->index_sens[i]];
/* pbar[i] = abs(data->p[i]); */ /*??? WHAT IS PBAR ???*/
}
flag = CVodeSetSensParams(solver->cvode_mem, data->p, NULL, NULL);
if (check_flag(&flag, "CVodeSetSensParams", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
flag = CVodeSetSensRho(solver->cvode_mem, 0.0); /* what is it? */
if (check_flag(&flag, "CVodeSetSensRhs1Fn", 1, stderr)) {
/* ERROR HANDLING CODE if failes */
return 0;
}
}
/* CVodeSetSensTolerances(solver->cvode_mem, CV_SS, */
/* solver->reltol, &solver->senstol); */
/* difference FALSE/TRUE ? */
flag = CVodeSetSensErrCon(solver->cvode_mem, FALSE);
if (check_flag(&flag, "CVodeSetSensFdata", 1, stderr)) {
return 0;
/* ERROR HANDLING CODE if failes */
}
return 1; /* OK */
}
time_series_t *read_data(char *file, int n_var, char **var)
{
int i;
char *name;
int n_data; /* number of relevant data columns */
int *col; /* positions of relevant columns in data file */
int *index; /* corresponding indices in variable list */
int n_time; /* number of data rows */
time_series_t *ts;
/* alloc mem */
ASSIGN_NEW_MEMORY_BLOCK(ts, 1, time_series_t, NULL);
/* alloc mem for index lists */
ts->n_var = n_var;
ASSIGN_NEW_MEMORY_BLOCK(ts->var, n_var, char *, NULL);
ASSIGN_NEW_MEMORY_BLOCK(ts->data, n_var, double *, NULL);
ASSIGN_NEW_MEMORY_BLOCK(ts->data2, n_var, double *, NULL);
/* initialize index lists */
for ( i=0; i<n_var; i++ )
{
ASSIGN_NEW_MEMORY_BLOCK(name, strlen(var[i])+1, char , NULL);
strcpy(name, var[i]);
ts->var[i] = name;
ts->data[i] = NULL;
ts->data2[i] = NULL;
}
/* alloc temp mem for column info */
ASSIGN_NEW_MEMORY_BLOCK(col, n_var, int, NULL);
ASSIGN_NEW_MEMORY_BLOCK(index, n_var, int, NULL);
/* read header line */
n_data = read_header_line(file, n_var, var, col, index);
ts->n_data = n_data;
/* count number of lines */
n_time = read_columns(file, 0, NULL, NULL, NULL);
ts->n_time = n_time;
/* alloc mem for data */
for ( i=0; i<n_data; i++ )
{
ASSIGN_NEW_MEMORY_BLOCK(ts->data[index[i]], n_time, double, NULL);
ASSIGN_NEW_MEMORY_BLOCK(ts->data2[index[i]], n_time, double, NULL);
}
ASSIGN_NEW_MEMORY_BLOCK(ts->time, n_time, double, NULL);
/* read data */
read_columns(file, n_data, col, index, ts);
/* free temp mem */
free(col);
free(index);
/* initialize interpolation type */
ts->type = 3;
/* calculate second derivatives */
for ( i=0; i<n_var; i++ )
if ( ts->data[i] != NULL )
{
if ( spline(ts->n_time, ts->time, ts->data[i], ts->data2[i]) != 1 )
return NULL; /* ran out of memory during spline routine */
}
ts->last = 0;
/* alloc mem for warnings */
ASSIGN_NEW_MEMORY_BLOCK(ts->mess, 2, char *, NULL);
ASSIGN_NEW_MEMORY_BLOCK(ts->warn, 2, int, NULL);
/* initialize warnings */
ts->mess[0] = "argument out of range (left) ";
ts->mess[1] = "argument out of range (right)";
for ( i=0; i<2; i++ )
ts->warn[i] = 0;
return ts;
}