Re: [lammps-users] MD simulations in hexagon prism unit cell
surendra jain <jainsk.iitkgp@...24...>
Tue, 19 Sep 2017 09:38:01 +0530
I am using hexagon prism unit cell. The boundaries of the simulation
cell is below :
Thus 1 to 6 marks the corners of my simulation cell.. The PBC in this
system is different than orthogonal or hexagonal system. I have to
change the neighbors calculation routine and PBC routine.
On 9/19/17, Andrew Jewett <jewett@...1937...> wrote:
> 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 f or that error
> message here:
> 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:
> (In moltemplate, this is called the "Data Boundary" section.)
> 2) using the "change_box" input script command. For details, see:
>> 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:
> and some nice videos here:
> If you are using moltemplate, the introduction/tutorial chapter (chapter
> 4) provides a list of helpful LAMMPS and VMD commands you will need.
>> Best Regards,
>> c boundary conditions,bnd you could use
>>> them to build a hexagonal system (or at least one that's -almost->
>>> ...however the shape of the of the simulation boundary box and the shape
>>> 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
>>> of arrangements on the moltemplate web page, (but of course, you don't
>>> to use moltemplate to set your simulation up this way)
>>> (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"
>>> Also see this example:
>>> On Sep 4, 2017 11:31 AM, "surendra jain" <jainsk.iitkgp@...24...>
>>> 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,
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