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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: surendra jain <jainsk.iitkgp@...24...>
Date: Sat, 16 Sep 2017 21:21:25 +0530

Dear Andrew,

  many thanks for your message. I have to modify the PBC criteria for
hexagon prism unit cell.  Can someone tell me which subroutines use
PBC. It will help me a lot.

Also, is neighbor list created for orthogonal box. Can I use it for
hexagon prism unit cell.

Best Regards,
Surendra


c boundary conditions,bnd 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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