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Re: [lammps-users] how to use VMD to better visulize the surface of a crystal
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Re: [lammps-users] how to use VMD to better visulize the surface of a crystal

From: ruiyan <r-yan14@...61...>
Date: Mon, 12 Jun 2017 02:13:33 +0800 (GMT+08:00)

Dear Axel,

Thanks for replying my email on weekend.

The reason is that I create some atoms exactly on the boundary of the box.  To move the box by a samll fraction, one way I can adopt is to difine a small box, then define a larger region and create atoms in this region. In this way, I can let the boundary of the box locate between two atom layers.  I can do this in x and y direction, however, in z direction,  because there are two atom layers in Al2O3  very close to each other and I want to create an interface located excatly between these two layers, so no matter how I move the box in z direction, one of the two layers will be very close to the boundary. Could you give me some suggestions on how to deal with it? Now I don't know whether atoms on the surface at the begining (shown in picture1) still stay on the surface in the end of the simulation (shown in picture2)?  

Is there any another way to achieve this? I mean is there any command I can use in VMD which can add Lx to an atom's x coordinate automically if the atom's x coordinate is less than xlo in dump file? We know that in a frame of a dump file, it is possible that an atom's x coordinate is less than xlo.  My understanding is if this happens, this means we should add Lx to the atom's x coordinate in a frame to get its real x coordinate. Is my understanding correct?   

Thanks and look forward to your reply. 


发件人: "Axel Kohlmeyer" <akohlmey@...24...>
发送时间: 2017-06-11 08:39:41 (星期日)
收件人: "严锐" <r-yan14@...61...>
抄送: "LAMMPS Users Mailing List" <>
主题: Re: [lammps-users] how to use VMD to better visulize the surface of a crystal

On Sat, Jun 10, 2017 at 6:02 PM, 严锐 <r-yan14@...61...> wrote:
Dear All, 

I'm using lammps to simulate Al2O3 single crystal and pure Al single crystal. My dump file contatins id, type, x, y, z. When I use VMD to visualize my dump file, I found that there were some isolated atoms on the surface of the box as shown in picuture_1, making the surface rough. My understandings is that this is because the coordinates of these atoms are out of the boundary of the box. If we check the dump file, we can see that the coordiantes of some atoms are less than xlo or greater than xhi.I want to know how to move these atoms back to the simulation box so that VMD can give a better visualization of the surface, with the surface of a crystal being as flat as a inner plane, which is shown in picture_2? To do this, what should be included in dump file?

​try dumping xu, yu, zu instead of x, y, z​.

you don't want to wrap them "back into the box"; that is already happening, but rather you don't want them to be wrapped back.

another issue could be, that you are creating atoms exactly on the box boundary. move the box by a small fraction of the lattice constant, say 20%, and these atoms may not be coming close to the box boundaries at all, so this all will become a non-issue.



Thanks and look forward to your reply.


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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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