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Re: Help with ODE solver
From: |
Marco Antoniotti |
Subject: |
Re: Help with ODE solver |
Date: |
Fri, 13 Sep 2002 10:28:21 -0400 |
Thanks a lot for the answer.
Let me give you some background on this little project of mine.
I have a set of ODE in textual form which I parse to generate
Octave/Matlab code. Generating the simple XDOT function to pass lsode
is easy. It is how to set up experiments with "discontinuity" in
parameters that is unclear to me.
> From: "John W. Eaton" <address@hidden>
> Date: Thu, 12 Sep 2002 19:18:38 -0500
> Cc: address@hidden, address@hidden
>
> On 12-Sep-2002, Marco Antoniotti <address@hidden> wrote:
>
> | Pardon my obtuseness. Do you mean that I will have to have a big 'if'
> | in the RHS function like
> |
> | if (t < t_crit_1)
> | ...
> | elseif (t_crit_1 <= t && t < t_crit_2)
> | ...
> | elseif (t > t_crit_k)
> | ...
> | end
> |
> | and call
> |
> | result = lsdot('RHS', intial_conditions, timesteps, [t_crit_1; t_crit_2
> ... t_crit_k]);
> |
> | ?
>
> Yes, that would be one way, but then you would need to make all those
> t_crit_N values global.
I thing I cannot avoid it. As it is, and because I need to be
selective about what I plot, I alread make the initial_contitions
global.
> It might make more sense to use a vector of
> values and a loop in your RHS function.
Sorry, but I do not understand this. Why would you want to do that?
> Or, you could vectorize it depending on how your time-dependent
> parameter values are stored.
Again I do not understand this.
> Perhaps someone else on the list can help you with the programming
> details.
I would appreciate this. Thanks in advance.
> My reason for responding in this thread was to point out that using
> tcrit with lsode is important if you have a discontinuity in the
> derivative due to changing parameter values. Simply breaking up the
> integration into intervals may not be sufficient because if you don't
> specify tcrit, lsode may integrate past your final time point and
> interpolate backward to find the final state values. If you have a
> discontinuity there, then the integrator may still have trouble,
> respond by reducing the step size to zero, and eventually fail.
Ok, I think I at least understand that.
Cheers
--
Marco Antoniotti ========================================================
NYU Courant Bioinformatics Group tel. +1 - 212 - 998 3488
715 Broadway 10th Floor fax +1 - 212 - 995 4122
New York, NY 10003, USA http://bioinformatics.cat.nyu.edu
"Hello New York! We'll do what we can!"
Bill Murray in `Ghostbusters'.
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- Re: Help with ODE solver, (continued)
- Re: Help with ODE solver, Douglas Eck, 2002/09/12
- Re: Help with ODE solver, John W. Eaton, 2002/09/12
- Re: Help with ODE solver, Marco Antoniotti, 2002/09/12
- Message not available
- Re: Help with ODE solver, John W. Eaton, 2002/09/12
- Re: Help with ODE solver, Marco Antoniotti, 2002/09/12
- Re: Help with ODE solver, John W. Eaton, 2002/09/12
- Re: Help with ODE solver, Marco Antoniotti, 2002/09/12
- Re: Help with ODE solver, John W. Eaton, 2002/09/12
- Re: Help with ODE solver,
Marco Antoniotti <=
- Re: Help with ODE solver, John W. Eaton, 2002/09/13
- Re: Help with ODE solver, Jon Davis, 2002/09/13
- Re: Help with ODE solver, Marco Antoniotti, 2002/09/13
- Re: Help with ODE solver, Martin Senator, 2002/09/12