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Re: [ESPResSo] analyze pressure and energy problems

From: Olaf Lenz
Subject: Re: [ESPResSo] analyze pressure and energy problems
Date: Mon, 15 Jun 2009 11:18:22 +0200
User-agent: Thunderbird (X11/20090409)


İbrahim İnanç wrote:
PID 24522 failed on node n0 ( due to signal 7.

Signal 7 is a bus error - very strange. How did you compile ESPResSo, and on what platform?

I want to simulate polybutadiene with 32 chains of 128 carbon atoms (32 rep. unit x 4). I changed the units in order to have the real atomic units. But somehow when I put analyze energy command it gives the below error message specially for higher integration steps or higher temperatures..
domain error: argument not in valid range
    while executing
"expr [analyze energy kinetic]"
    ("while" body line 8)
    invoked from within
"while { $i<$n_cycle} {

Can you please send the ESPResSo-script that you have been using? It is very hard to debug the problem as long as we don't know any more facts. From the description, I would guess that the problem is that you try to use atomic units. ESPResSo works best when all numbers are in the order of 1. When you use parameters that are several orders of magnitude below or above 1, it might happen that the algorithms become numerically unstable, or even that some heuristics used by ESPResSo to check the validity of the parameters don't work. This means, that you should *not* use SI units when doing a molecular simulation, instead use the more natural units, like Angström for lengths, and fs for times.


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