Re: [SOSlib-discuss] equivalent to observablesArray ?

[Rainer M. <ra...@tb...>]

Hi Eric,

In general, the IntegratorInstance_getVariableValue is the only way an 
external application is supposed to use to retrieve values from the model 
between IntegratorInstance_integrateOneStep calls.

In the new version (CVS) this function also makes sure that the retrieved 
values are up-to-date (by evaluating assignment rules for values that 
might have changed)!

Calling engine->data->value[i] directly is not considered save (although 
your way gave correct results!), and also such internal data structures 
might change with upcoming releases, while the interface function should 
stay the same!


The observables array was used to optimize the updating of rules, i.e. to 
only update assignment rules required for a set of "observables", and 
thereby consider assignments that are already up-to-date. Since there is 
no restriction on ordering of rules in the new SBML version, the old 
approach wouldn't have worked that easily anymore.
Also the observables could have let to _getVariableValue returning wrong 
values, if the user/application is not aware of the 
observables-requirement.

Now this updating of remaining rules has been moved to _getVariableValue 
interface function, which only calls it once between _integrateOneStep and 
remembers that rules are up-to-date now.
And for the vast majority of models there would be no increase in 
efficiency to restrict this update to a set of observables.

Thus, efficiency-wise the observables array is not necessary anymore. You 
can just use _getVariableValue for any value you like.


It is however a design decision. Do we want to provide direct access at 
least to data->value ?

In that case, I could reintroduce the observables, which an application 
has to preset to make sure these are kept up-to-date independent of 
calling _getVariableValue.


Opinions?


Rainer



On Mon, 27 Oct 2008, Eric Fernandez wrote:

> Hi again :)
>
> I have a question regarding the recent CVS version.
>
> Before it was possible to filter out model parameters from model species
> using :
>
> if (om->observablesArray[i]) {
>   fprintf(outfile, "%g ", engine->data->value[i]);
> }
>
> but now the observablesArray has disappeared. How is it possible to get
> an output equivalent to previous version?
>
> Thanks,
> Eric
>
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