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Re: [lammps-users] Simulation warning
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Re: [lammps-users] Simulation warning


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 19 Oct 2017 14:34:37 -0400

On Thu, Oct 19, 2017 at 1:01 PM, A. M.M <alaa.murar@...24...> wrote:
> بسم الله الرحمن الرحيم
>
> Hello,
>
> I run a simulation for beads-springs polymer(chain) only and I used a pair
> style lj/cut/coul/debye/omp, and I set the cutoff for debye equal to the
> length of the chain plus a distance so the net one is 557.6 angstrom ( I
> used real units ). I used shrink boundary condition for all dimensions, and
> the nsq style for neighbor build, and a 3.0 for skin.
>
> The simulation run well, but the following warning appeared:

i would not expect that simulation to run as well as it could. i would
expect it to run very slow. how large is your simulation cell?

>
> WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms
> (../domain.cpp:937)
>
> but no atom was lost. Also, there a few dangerous neighbor builds compared
> to the total one.
>
> Does this warning dangerous? and how can I avoid it ?

your choice of pair style makes not much sense or rather your cutoff
is *massively* oversized and probably your system too small (so you
may be plagued by finite size effects).
you should be running with lj/cut/coul/long and ewald or pppm and a
meaningful cutoff would be in the neighborhood  of 12 \AA.
with a large cutoff you are growing the cost of your computation with
O(r**3) and will have to manage huge neighbor lists and massive
amounts of communication through updating ghost atom data.

also, nsq neighborlist builds are inefficient for larger cells and the
default binning is to be preferred.

axel.



>
> Thank you.
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.