Re: [SOSlib-discuss] copyVariableState() and setVariableValue() issues[Scanned]

[Eric F. <efe...@ph...>]

Hi,

Oh well congratulations! Are you joining some famous Systems Biology
group there ?
I wish you a very good time there. With excellent and healthy food!

Regards,
Eric 

> -----Original Message-----
> From: Rainer Machne [mailto:ra...@tb...] 
> Sent: 17 November 2008 01:45
> To: Eric Fernandez
> Cc: sbm...@li...
> Subject: Re: [SOSlib-discuss] copyVariableState() and 
> setVariableValue() issues[Scanned]
> 
> Hi Eric,
> 
> sorry for the late reply, I have just moved to Japan for a year.
> 
> On Sat, 8 Nov 2008, Eric Fernandez wrote:
> 
> >
> > Hi,
> >
> > I reply to myself regarding the usage of setVariableValue() 
> : indeed 
> >it works as intended. However, I get the same problems than with
> >copyVariableState(): when the integration is solved with a Jacobian 
> >matrix, I get a convergence test error as soon as I do the first 
> >integration step. I wonder why there is a problem, shouldn't an 
> >integrator instance behave normally if the initial conditions are 
> >changed?
> 
> I guess, I should have a look at copyVariableState, if it 
> still works as intended after all the changes made.
> 
> However, I think the situation you described can happen. The 
> new initial conditions might put the system close to some 
> hard-to-solve stiff state, and a running solver might have 
> it's internal time steps etc. already set-up for this 
> situation, while a newly starting solver has problems with 
> the same conditions. Maybe you could try to play with the 
> error tolerances and printstep size?
> 
> But you are right, the CVodeReInit caused by events should 
> have the same or similar effects on an already running itnegrator.
> 
> Are there any news regarding this problem?
> 
> Rainer
> 
> >
> >
> > Eric
> >
> >
> > -----Original Message-----
> > From: Eric Fernandez [mailto:efe...@ph...]
> > Sent: Fri 11/7/2008 12:36 PM
> > To: sbm...@li...
> > Subject: [SOSlib-discuss] copyVariableState() and 
> setVariableValue() 
> > issues[Scanned]
> >
> > Hi,
> >
> > I am wondering if there are not issues with copyVariableState(), 
> > probably I do not use it correctly.
> >
> > I am trying to run a model (very large and complex, using 
> many events) 
> > for a couple of steps, and then want to transfer the 
> species values to 
> > a new, fresh integrator instance, and run again using the final 
> > variable state of the first integrator instance as the initial 
> > conditions of the second integrator instance. (That is to 
> simulate a 
> > checkpoint.)
> >
> > First method I use is copyVariableState(). The problem is that very 
> > often I get convergence test errors and other weird stuff (some 
> > species becoming negative) that happen for particular values of the 
> > steps used in the first instance. Some step values work 
> like a charm, 
> > some others lead to these issues. Am I doing this wrong ?
> >
> > The second method, was to dump all the species names/values 
> at the end 
> > of the first instance integration in an array. Then I 
> create a second 
> > integrator instance and use a loop over my array to initialise all 
> > corresponding values, using setVariableValue(). The really 
> weird stuff 
> > here, is that when I start again the integrator, it is as if it were
> > reset: it uses the initial conditions of the model, not the one set 
> > with setVariableValue(). Is it normal ? Or do I make 
> something wrong here ?
> >
> > Thanks for the help,
> > Eric
> >
> > 
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