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Re: [lammps-users] Problem with defining correct cubic simulation box
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Re: [lammps-users] Problem with defining correct cubic simulation box


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 22 Apr 2018 05:59:01 -0400

On Fri, Apr 20, 2018 at 6:49 PM, Khourshaei Shar, Ali
<akhoursh@...6666...> wrote:
> Dear LAMMPS users,
>
>
> suppose that the lattice structure of your material is monoclinic such as
> SiC, SiN and etc. However, you have to do your simulation on a cubic
> simulation box.

no, you don't. LAMMPS can handle orthogonal and triclinic box shapes.

> For the sake of thism I used the following code, define a
> cubic region and fill it with atoms as follow:

[...]

> So, my problem is that the structure doesn't look correct for the sake of
> periodicity. I attached an image of it and circle around the section of the
> boundary that as I switch on show periodic image in Ovito, it doesn't look
> correct. I mean the structure doesn't look uniform as we go from left of the
> boundary to the right of it.

that is difficult to tell from that perspective. it is very likely,
that this is an optical illusion, caused by a tiny inconsistency in
the cell lengths and assigned lattice positions plus the lack of depth
perception.

i would run a minimization and record a trajectory. if there are
really issues with periodicity, you should see notable deformations at
those perceived to be incorrect periodic replication areas.

axel.

>
>
>
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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.