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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, 18 Sep 2017 15:44:32 -0700

On Sep 17, 2017 3:18 AM, "surendra jain" <jainsk.iitkgp@...24...> wrote:
. I want to know if image flags are used
during MD simulation.

Why?  Is LAMMPS giving you an error message or warning message about your image flags?  What is that error message?  Have you looked for that error message here:
 
http://lammps.sandia.gov/doc/Section_errors.html

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.

On 9/16/17, surendra jain <jainsk.iitkgp@...24...> wrote:
> hexagon prism unit cell.  Can someone tell me which subroutines u
> PBC. It will help me a lot.

You control the boundaries of the box either by 
1) editing your DATA file (assuming you are using a LAMMPS DATA file to store the initial coordinates of the atoms in your system). Near the top of the data file, there is a "Boundary" section.  You control the size and shape of the boundary there.  See:
http://lammps.sandia.gov/doc/read_data.html
(In moltemplate, this is called the "Data Boundary" section.)

2) using the "change_box" input script command.  For details, see:
http://lammps.sandia.gov/doc/change_box.html


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

Why are you worried about how LAMMPS calculates the neighborlist?  LAMMPS can simulate systems with rectangular or triclinic/hexagonal boundary conditions, and LAMMPS should calculate the neighborlist correctly regardless.  In my previous post I suggested it might be more convenient to use rectangular boundaries instead of hexagonal boundaries, but both are possible in LAMMPS.

It seems to me that you should look at some of the LAMMPS examples.  I found the "peptide" exam to be particularly helpful. 

There is a list of turning here:

http://lammps.sandia.gov/tutorials.html

and some nice videos here:
https://youtube.com/watch?v=GXA2PyqKYdY
https://m.youtube.com/watch?v=ZMiveX6n-1w

 If you are using moltemplate, the introduction/tutorial chapter (chapter 4) provides a list of helpful LAMMPS and VMD commands you will need.

Cheers
Andrew


> 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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