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Re: [lammps-users] MD simulations in hexagon prism unit cell
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Re: [lammps-users] MD simulations in hexagon prism unit cell


From: Andrew Jewett <jewett@...1937...>
Date: Mon, 4 Sep 2017 14:53:15 -0700

Dear Surendra

LAMMPS allows you to use triclinic boundary conditions, and you could use them to build a hexagonal system (or at least one that's -almost- hexagonal). 
http://lammps.sandia.gov/doc/read_data.html

...however the shape of the of the simulation boundary box and the shape of the unit cell of your crystal need not be the same.  In your case, I'm guessing it might be both easier and slightly more computationally efficient to simulate a hexagonal crystal using rectangular boundary conditions.  To clarify what I mean, there are some pictures of these kinds of arrangements on the moltemplate web page, (but of course, you don't have to use moltemplate to set your simulation up this way)

http://moltemplate.org/visual_examples.html#membrane+protein
   (Scroll to the right hand side of the page.  The blue wireframe box shows the simulation boundaries, and they are defined in the "system.lt" file)  
Also see this example:
http://moltemplate.org/visual_examples.html#nanotube+water

Cheers
Andrew

On Sep 4, 2017 11:31 AM, "surendra jain" <jainsk.iitkgp@...24...> wrote:
Dear all,

  I have a system of carbon model in hexagon prism unit cell. I would
like to study diffusion of Nitrogen in the carbon model. Lammps does
not support hexagon prism unit cell. Can someone please point out how
to start/which part of the LAMMPS need to change.

I think the only portion to change is the PBC in LAMMPS. Also, can
someone please tell me if neighboring list being created depend on the
type of simulation box.

Best Regards,
Surendra

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