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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: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 10 Jun 2017 20:39:41 -0400

On Sat, Jun 10, 2017 at 6:02 PM, 严锐 <r-yan14@...612......> 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@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.