Hi Eryk,
W Eryk Wolski wrote:
> Hi...
>
> It might be that I have asked this question a few months ago on this
> list but can not recall the answer...
>
> My question is with regard to:
>
> integratorInstance->data ->nsens
> integratorInstance->data->neq
> integratorInstance->data->sensitivity
> where data is cvodeData.
>
> The model I have 5 global parameters
> and 8 (outputs) equations, than:
>
> neq == 8 True
> nsens == 5 False nsens is 6.... what the 6 th sensitivity stands for?
The 6th sensitivity is probably the compartment, which is treated as a
constant parameter in the odeModel.
Have you noticed that you can now set the parameters for sensitivity
analysis?
Use
CvodeSettings_setSensParams(cvodeSettings_t *, char **sensIDs, int nsens);
to pass a list to cvodeSettings_t,
where sensIDs is an array of strings containing the SBML IDs of the
parameters to which you want to calculate sensitivities and nsens is the
size of this array.
Unfortunately, there is no other way to avoid calculating sensitivities
for compartments. This is always included in the default sens.analysis,
as on the ODE level we do not distinguish between compartments and other
model parameters anymore.
> and the dimension of
> integratorInstance->data->sensitivity
> is neq x nsens
>
> and are the rows 2-6 or the 1-5 are those i am looking for?
On the level of the integratorInstance you can get the name of the
parameter via
char* IntegratorInstance_getSensVariableName(integratorInstance_t
*engine, int i)
where 0 <= i < nsens.
On the level of SBMLResults you can use
char *SBMLResults_getSensParam(SBMLResults_t *res, int i)
where again 0 <= i < nsens.
You can get nsens with
SBMLResults_getNumSens(SBMLResults_t *res)
ODEModel_getNsens(odeModel_t *);
For the default case nsens = nconst. For the non-default case the
application has set nsens itself via above function.
I just realized that above functions are named differently and that
CvodeSettings and IntegratorInstance are missing the Nsens function.
These should be added to the API!
For now I have added a general comment on refactoring, coordinating and
streamlining API functions for all our structures (odeModel,
integratorInstance, cvodeSettings) to the list at
http://www.tbi.univie.ac.at/wiki/index.php/SOSlibDevel#API_reorganization
Rainer
>
>
> Eryk
>
>
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