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.lo...@kitware.com>
> On Tue, May 21, 2013 at 5:58 AM, 李文凡 <limurphy1...@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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