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Re: [lammps-users] remove atoms which cross periodic boundaries (keeping PBC)
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Re: [lammps-users] remove atoms which cross periodic boundaries (keeping PBC)


From: Steve Plimpton <sjplimp@...24...>
Date: Wed, 25 Apr 2018 15:03:05 -0600

You could also possibly use fix evaporate, perhaps in concert
with the fragment identification.

Steve

On Wed, Apr 25, 2018 at 10:11 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
On Wed, Apr 25, 2018 at 11:59 AM, Valerio Sorichetti
<valeriosorichetti@...29....> wrote:
> Dear LAMMPS users,
>
> I am running the following simulation (with periodic boundary conditions,
> PBC):
>
> -I start from a fully connected polymer network (FENE bonds)
> -I break a certain number of bonds randomly
> -I let the network relax
>
> During this procedure, a certain number of free polymer segments will be
> formed, which will diffuse freely. What I want to do is to get rid of these
> free segments.
>
> What I thought of doing is letting the simulation run for a long enough time
> and delete all the atoms which cross the periodic boundaries.
>
> In an older post, it was suggested to use fixed boundary conditions (FBC)
> and then allow for lost atoms, i.e.
>
> thermo_modify   lost   ignore
>
> However, this solution doesn't work in my case because the bond topology
> takes into account the PBC (i.e. if I just change the BC from PBC to FBC
> this will result in some atoms being bonded to others which are on the other
> side of the box, and therefore in an error).
>
> How can I obtain the desired result?

please check out the compute fragment/atom command. this should allow
to identify the different fragments and then you can reference the
corresponding fragment ids in an atom style variable to have all
undesired atoms not matching the fragment id of the core polymer
(which would be the largest fragment) deleted.

axel.


>
> Best regards,
>
> Valerio
>
> PS: I am aware that an option would be to manipulate directly the output
> file, removing all the atoms with nx,ny or nz value different from 0 (see
> here for the notation). However, I would like to find a solution using
> LAMMPS.
>
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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