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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: Sun, 17 Sep 2017 15:48:25 +0530

Dear Andrew,

  many thanks for your message. I want to know if image flags are used
during MD simulation. I cannot think of providing image box for
hexagon prism unit cell (not hexagonal). I can wrap the coordinates
back into simulation box, but it is not trivial to set image flags for
my system.

Best Regards,
Surendra


On 9/16/17, surendra jain <jainsk.iitkgp@...24...> wrote:
> 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 u
> 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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>