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Re: [lammps-users] about shake atoms error
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Re: [lammps-users] about shake atoms error

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 10 Jul 2017 06:57:14 -0400

On Sun, Jul 9, 2017 at 4:58 PM, reza N.Z <mrn.nz91@...24...> wrote:
> Dear lammps Users
> I have faced "shake atoms %d %d %d missing on ..." error in a simulation
> with slab correction. I know that one of the molecules passes the boundary
> which the slab-correction is assigned. Losing this molecule does not have
> considerable influence on the simulation though. How can I pass over this
> issue without changing the simulation box?

when using slab correction, you must never let atoms get even close to
the box boundaries.
when you use the kspace_modify command, LAMMPS increases the box
length in z-direction. this added space must not have any charges in
them. the simplest way to prevent this, is to place a wall on the
original box boundary with fix wall.

> I also used "thermo_modify" command with "lost ignore" option and it did not
> work.



> Thank you so much.
> Best regards,
> Reza
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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.