[SOSlib-devel] piecewise ... (fwd)

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

Hi All,

for the record, and for anyone interested in bug fixing :), i forward this 
email to the list.

Again or still, we seem to have a piecewise bug. The reason for the 
strange behaviour described by Nicolas below is unclear.

A piecewise expression used in an assignment rule contains the "time". The 
respective expression seems to be set true at time 57... while it should 
only become true at time 60.

The only suspicion I have is that the assignment rule is not updated 
correctly and that the rule still has some value which it took in an 
internal CVODE evaluation when it internally was already at time 60 for 
evaluating f.
Andrew, is it possible that your priority for assignment rule evaluation 
doesn't account for rules that contain "time"?

I will look at it next week but maybe you have an idea.

Rainer


---------- Forwarded message ----------
Date: Tue, 12 Sep 2006 18:03:20 +0100 (BST)
From: Nicolas Le Novere <le...@eb...>
To: ra...@tb...
Subject: piecewise ...

Dear Rainer,

We are still working on the problematic model that led us to ask-you
to modify SBMLodeSolver for piecewise functions (we are doing other
things as well, don't worry :-)

I attach a model that should be fine. I tested it without rule, and
with only the assignment rule for Sstar. In both case, the model
worked perfectly. Now, with the piecewise function (only one piece for
the moment), we encounter all kinds of problems:

For some reason, at t=57, Sstar jumps from 0.012 to 14.45, the value
it will take after the piecewise jump for calcium at t>60. But the
calcium is still unchanged!

Then, after t=60, even if Sstar increased 0.012 to 14.45, the
reactions involving it remain unchanged, until t=62.44.

Is-it a problem of output only? Is-it a problem in the patching of
SBMLodeSolver?

I join the SBML and the output of

odeSolver -w --time 100 --printstep 1000 
dAlcantara_Bidirectional_Plasticity_CorrectedOnePiece.xml

(renamed .clean to go through the mail filters)

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521,  Fax: +44(0)1223 494 468,  Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov, AIM: nlenovere,  MSN: nle...@ho...