Re: [SOSlib-devel] Parameters with undefined values in odeSolver

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

ok, sorry.

here is a proper patch file.

r


On Wed, 7 Jun 2006, Rainer Machne wrote:

> Hi Michael,
>
> Two patch files for the bug you observed can be found in the attachment.
>
> Basically, one needs to avoid the dangerous
>
> * Parameter_createWith(.... Parameter_getValue ...)
>
> for params, species and compartments in odeConstruct.c,
> (the code which constructs a new internal SBML model, in which reactions are 
> replaced by rate rules (i.e. ODEs))
>
> and not use
>
> * Parameter_getValue
>
> in cvodedata.c,
> (when writing initial values (ODE variables) or constants (ODE parameters) to 
> the data structure used by the integrator.)
>
> When no value is available, a fatal error is stored, and
> IntegratorInstance_create(...) returns NULL.
>
> This patch doesn't care however, if a parameter that is defined by an 
> assignment rule (a in our example) does not have a value, as this value would 
> be overruled by the assignment anyways. I think, this should be correct.
>
>
> The output of our command-line program now should be:
>
> odeSolver/odeSolver valtest.xml Fatal Error     20000   No value found for 
> parameter b
> Exit 1
>
>
> Rainer
>
>
>
>
> On Tue, 6 Jun 2006, Michael Hucka wrote:
>
>> You're welcome, but thank you for creating the most
>> excellent SBML ODE Solver!
>> 
>> MH
>> 
>>  raim> Hi Michael
>>  >>
>>  >> It sounds like the short-term solution is for SOSlib to
>>  >> implement this:
>>  >>
>>  BB> ... the value returned by getValue() should *not* be
>>  BB> used / trusted if isSetValue() returns false
>>  BB> (zero)....
>>  >>
>>  >> The long-term solution is that libsbml 3 will
>>  >> incorporate a check.
>>  >>
>>  >> Is that correct?
>>  raim>
>>  raim> Yes, I will try to find out where our code needs to
>>  raim> be fixed and post detailed instructions for changing
>>  raim> 1.6.0 code on our website.
>>  raim>
>>  raim> Unfortunately, we don't have a separate CVS branch
>>  raim> for bugfixes of the current release, so the CVS will
>>  raim> only contain the bugfix for the current development
>>  raim> version of the code.
>>  raim>
>>  raim> Thanks again for finding and reporting this quite
>>  raim> serious bug!
>>  raim>
>>  raim> Rainer
>>  raim>
>>  raim>
>>  raim> On Thu, 1 Jun 2006, Michael Hucka wrote:
>>  raim>
>>  raim>
>>  raim>
>>  raim>
>>  raim>
>>  raim>
>>  raim>
>>  >>
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