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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: Tue, 19 Sep 2017 09:38:01 +0530

Dear Andrew,

  I am using hexagon prism unit cell. The boundaries of the simulation
cell is below :


                                       5
                               2              1

                                       0

                                3             4

                                       6

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.

Best Regards,
Surendra


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:
>
> 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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>>
>