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

From: 严锐 <r-yan14@...61...>
Date: Sun, 11 Jun 2017 06:02:33 +0800 (GMT+08:00)

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?

Thanks and look forward to your reply.


Attachment: picture_1.JPG
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Attachment: picutre_2.JPG
Description: JPEG image