Re: [SOSlib-discuss] ODEModel_createWithObservables

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

Hi,

I think we can get rid of the "observables" all together. I have moved 
update of all assignment rules - even those which are not required to 
solve the system - to the two cases were required:

a) with option StoreResults: all values are stored, so all rules need to 
be updated anyways

b) IntegratorInstance_getVariableValue: if an assigned value is 
requested specifically, then assignment rules are updated (but only 
once, if the function is used several times at the same integration step!).

So if you solve without the StoreResults option, and don't use 
getVariableValue for assigned values (rate laws, values only in the 
model for observation purposes), the solver will always only update the 
required rules.

At a later point also the complete rule evaluation for above cases could 
be optimized by storing the dependency graph between assignments and use 
a recursive evaluation through this graph ONLY for the requested values.

As a conclusion, "observables" to optimize solver performance is not 
required anymore, and I will remove this functionality completely.

Any objections?

Rainer




Rainer Machne wrote:
> Hi,
> 
> Is anyone using the functions to create an ODEModel "WithObservables"?
> 
> I plan to move this to CvodeSettings_setObservables (and to move the 
> respective structures and functions to CvodeData).
> 
> The reason is, that odeModel otherwise only depends on the SBML input, and 
> defining "observables" fits more natural to the input settings.
> Also, one odeModel can then be run with different observables sets, and 
> observables don't depend on the odeModel anymore.
> 
> fyi, the rule-ordering, which made observables necessary, is currently 
> being replaced with a topological sorting-based ordering (to allow SBML 
> L2V2 initial assignments, and lost constraints on rule ordering).
> 
> Is that a problem for anyone?
> 
> Thanks,
> Rainer
> 
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