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Re: [lammps-users] Changing boundary conditions from periodic to non-periodic to simulate shock in a polymer
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Re: [lammps-users] Changing boundary conditions from periodic to non-periodic to simulate shock in a polymer


From: Steve Plimpton <sjplimp@...24...>
Date: Fri, 14 Jul 2017 07:52:16 -0600

I think you could do something like the following:

a) dump the atoms to a dump file with unwrapped coords
b) use the change_box command to convert to non periodic BC
c) use the read_dump command to read back in the
    unwrapped coords


Steve

On Thu, Jul 13, 2017 at 3:21 PM, S. Ramaswami <rsubrah@...1509...> wrote:

I mean that if I have a molecule containing a four-carbon backbone, and it appears in the cell with PBCs like this ( where the cell boundaries are denoted by || and bonds by -- ):

||-C--H  H--C--C--C-||

with the shock propagating from left to right,
then I want to move atoms so the molecule appears like this:

||H--C--C--C--C--H||

Actually, each molecule in my model has over 2000 atoms.

Regards,
Ramaswami.



________________________________
S. Ramaswami  |  Research Associate
College of Engineering, Computing and Applied Sciences

238 EIB  |  Clemson, SC 29634-0921
rsubrah@clemson.edu  |  864.656.5639

Clemson University






From: Axel Kohlmeyer <akohlmey@...24...>
Sent: Thursday, July 13, 2017 3:45 PM
To: S. Ramaswami
Cc: lammps-users@...396...sourceforge.net
Subject: Re: [lammps-users] Changing boundary conditions from periodic to non-periodic to simulate shock in a polymer
 


On Thu, Jul 13, 2017 at 2:59 PM, S. Ramaswami <rsubrah@...6993......> wrote:

Dear All,

I have an equilibrated polyurea model with periodic boundary conditions applied (thanks to valuable advice earlier), and intend to remove the periodic boundary conditions along one direction before simulating a shockwave through the model. Is there a way to use LAMMPS to "unwrap" the model in that direction when changing the boundary conditions? I realize I should equilibrate the model again before simulating the shockwave.

what do you mean exactly by "unwrap"? can you perhaps provide a little ASCII-art graph or a little drawing?

axel.
 

Regards,
Ramaswami.


________________________________
S. Ramaswami  |  Research Associate
College of Engineering, Computing and Applied Sciences

238 EIB  |  Clemson, SC 29634-0921
rsubrah@clemson.edu  |  864.656.5639

Clemson University




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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.

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