Dear Dave, 

Thank you for your follow-up.

For "rotation", I mean I drag the cell (pressing the right bottom of my mouse),
so it can be rotated around certain axis. 

If it is due to PBC, then how could I fix the defect position?

Thank you again!

Sincerely,
Murphy   


2013/5/21 David Lonie <david.lonie@kitware.com>
On Tue, May 21, 2013 at 5:58 AM, Z <limurphy1985@gmail.com> wrote:
> Dear Avogadro users,
>
> I am visualizing a supercell containing two defect sites, but after rotating
> the
> cell, the defect site changes place! It is really terrifying as I can not
> determine
> the exact defect site by viewing it. As shown in the attached files, in
> POSCAR.jpg,
> the defect at the right-up side is located at the second top atomic layer,
> but after I rotate the
> cell, as shown in POSCAR2.jpg, the defect site shifts to the first top
> layer.
>
> Is this problem related to periodic boundary
> condition? Does anyone know the reason of this problem and how to determine
> the defect
> site by Avogadro?
>
> Thank you very much, and very much looking forward to your help!

It looks like it might be related to periodic boundaries and wrapping
the atoms back into the unit cell. What do you mean by "rotating the
cell"? Are you just moving the camera, or are you modifying the
structure?

Dave

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