/* initialize sensitivity initial values at time 0 */
int CvodeData_initializeSensitivities(cvodeData_t *data,
cvodeSettings_t *opt,
odeModel_t *om, odeSense_t *os)
{
int i, j, nsens;
/* 0. catch default case, no parameters/variables selected */
if ( opt->sensIDs == NULL ) nsens = om->nconst;
else nsens = opt->nsens;
/* 1: free former sens. results, if different number is requested */
if ( data->nsens != nsens && data->sensitivity != NULL )
CvodeData_freeSensitivities(data);
/* 2: create cvodeData and odeModel structures */
if ( data->sensitivity == NULL )
{
CvodeData_allocateSens(data, om->neq, nsens); /* why not data->neq ? */
if ( data->sensitivity == NULL ) return 0;
}
/* do FIM stuff */
if ( opt->doFIM )
{
if ( data->FIM == NULL )
{
ASSIGN_NEW_MEMORY_BLOCK(data->FIM, nsens, double *, 0);
for ( i=0; i<nsens; i++ )
ASSIGN_NEW_MEMORY_BLOCK(data->FIM[i], nsens, double, 0);
}
else
{
for ( i=0; i<nsens; i++ )
/* initialize cvodeData from cvodeSettings and odeModel (could be
separated in to functions to further support modularity and
independence of data structures */
int
CvodeData_initialize(cvodeData_t *data, cvodeSettings_t *opt, odeModel_t *om)
{
int i, j;
/* data now also depends on cvodeSettings */
data->opt = opt;
/* initialize values */
CvodeData_initializeValues(data);
/* set current time */
data->currenttime = opt->TimePoints[0];
/* update assigned parameters, in case they depend on new time */
for ( i=0; i<om->nass; i++ )
data->value[om->neq+i] = evaluateAST(om->assignment[i],data);
/*
Then, check if formulas can be evaluated, and cvodeData_t *
contains all necessary variables:
evaluateAST(ASTNode_t *f, ,data) will
ask the user for a value, if a a variable is unknown
*/
for ( i=0; i<om->neq; i++ )
evaluateAST(om->ode[i], data);
/* create structures for sensitivity analysis */
if ( opt->Sensitivity ) {
/* the following can later be called with numbers from
sensitivity Settings inputs */
if ( data->sensitivity == NULL ) {
CvodeData_allocateSens(data, om->neq, om->nconst);
RETURN_ON_FATALS_WITH(0);
}
/* (re)set to 0.0 initial value */
for ( i=0; i<om->neq; i++ ) {
for ( j=0; j<om->nsens; j++ ) {
data->sensitivity[i][j] = 0.0;
}
}
}
/* Now we should have all variables, and can allocate the
results structure, where the time series will be stored ... */
/* allow results only for finite integrations */
opt->StoreResults = !opt->Indefinitely && opt->StoreResults;
/* free former results */
if ( data->results != NULL )
CvodeResults_free(data->results);
/* create new results if required */
if ( opt->StoreResults ) {
data->results = CvodeResults_create(data, opt->PrintStep);
RETURN_ON_FATALS_WITH(0);
if ( opt->Sensitivity ) {
CvodeResults_allocateSens(data->results, om->neq, om->nconst,
opt->PrintStep);
/* write initial values for sensitivity */
for ( i=0; i<data->results->neq; i++ )
for ( j=0; j<data->results->nsens; ++j )
data->results->sensitivity[i][j][0] = data->sensitivity[i][j];
}
RETURN_ON_FATALS_WITH(0);
}
return 1;
}
