[Pw_forum] internal position after relax
paulatto at sissa.it
Mon Mar 30 11:28:35 CEST 2009
On Mon, 30 Mar 2009 11:21:17 +0200, Djani Ait Aissa Hania <djaithania at yahoo.fr> wrote:
> dear all,
> after the relaxationof my structure, I noticed the position of one
> oxygens atom along the z-direction became greater than celldm(3) wich
> is physically impossible.
don't worry. Your system is composed of a unit cell, described by three vectors, and a basis, describing the atomic positions. There is no constrain on the basis; as periodic boundary conditions even if you put the atoms outside of the cell some there wil be a periodic replica that's inside. This is all done automatically by the software (mostly in reciprocal space, using structure-factor phases).
It is very common to put atoms out of the unit cell (often with negative coordinates!) when doing molecules, a bit les when doing bulk crystal, nevertheless there is nothing wrong with it.
If you feel uncomfortable you can scale the atom back into the cell by subtracting celldm(3) to its z-coordinate.
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