[ase-users] Arranging atoms in the cell of a POSCAR file (Clemens Barth)

[John Kitchin]

You want something like this:

https://wiki.fysik.dtu.dk/ase/ase/atoms.html#ase.atoms.Atoms.center

Or you can just translate the atoms so they are a "lump" in the center of
your unit cell.  There is no need to change the order of the atoms.

John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu



On Sun, Apr 7, 2013 at 6:00 AM, <ase-users-request at listserv.fysik.dtu.dk>wrote:

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>    1. Arranging atoms in the cell of a POSCAR file (Clemens Barth)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Sat, 06 Apr 2013 13:28:44 +0200
> From: Clemens Barth <barth at root-1.de>
> Subject: [ase-users] Arranging atoms in the cell of a POSCAR file
> To: ase-users at listserv.fysik.dtu.dk
> Message-ID: <516006EC.3090507 at root-1.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all.
>
> I have a POSCAR file, which describes the positions of atoms within a
> cell. When I load this
> file with, e.g., VMD the atoms are somewhat split up into groups. For
> instance, one part is located
> at the upper border of the cell along +z whereas the other part is at
> the lower border of the
> cell along -z - the atoms do not form one complete structure as one
> would expect. However, when
> repeating the cell all is okay - the structure is well represented. -
> somebody told me that this 'problem'
> is somewhat normal when doing VASP calculations
>
> However, due to some specific reasons I would like to rearrange the atom
> positions such that they
> are centered in the cell and that they are together forming one complete
> structure.
> Is there a mean to do this by some ASE function? Is there some function,
> which makes some
> 'order' in the cell without destroying the structure itself?
>
> Any help is highly appreciated.
>
> CB.
>
>
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