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Re: [ESPResSo] Restarting a simulation with clusters of particles

From: Lorenzo Isella
Subject: Re: [ESPResSo] Restarting a simulation with clusters of particles
Date: Thu, 3 Apr 2008 12:25:31 +0200

> What do you mean by "Espresso does not understand that the particles are
>  not far away"? What does ESPResSo do that you didn't expect?

What I mean is the following: say that simulation 1 returns 10
particles which are strongly bound together in a single aggregate.
I save what I call unfolded positions of the particles (which are
outside the box) and use them as an input for simulations 2 (which has
the same periodic box as computational domain).
Well, in this case I see an unphysical fragmentation of the aggregate
ever since the beginning of simulation 2.
However, if I start simulation 2 with the same output of simulation 1,
but this time folded inside the box, then everything goes fine.
So, my mistake not to have checked that more carefully.
What is probably tricky, but I think I  am sorting that out, is to run
simulation 2 on a larger box than simulation 1 and still use the
output of simulation 1, but I want to try out a few things and only if
they do not work post again on the list.


>  The only thing that comes to my mind that might be your problem: did you
>  set the system size BEFORE you load the particle coordinates? If you
>  first set the particle coordinates, and only afterwards the system size,
>  the coordinates will be changed when changing the system size, which
>  might lead to unexpected results.
>  Olaf
>  Version: GnuPG v1.4.6 (GNU/Linux)
>  Comment: Using GnuPG with Mozilla -
>  iD8DBQFH9KkitQ3riQ3oo/oRAtVrAKCrSzmMRq15B8hrrlIUg+Y+flFVYQCeIQXT
>  d+V5bU5BAS9qYZQGfQqqD3g=
>  =ESAb
>  -----END PGP SIGNATURE-----

It is hard to want something you cannot describe.

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