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

[John Kitchin]

You could get the scaled positions, and subtract 1 from each element that
is greater than 0.5, then set those as the new scaled positions. That is
the same as translating by unit cell vectors, and will result in all scaled
positions being between -0.5 and 0.5 (some outside the unit cell).


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 Mon, Apr 8, 2013 at 2:15 AM, Clemens Barth <barth at root-1.de> wrote:

>  Dear John.
>
> You want something like this:
>
> https://wiki.fysik.dtu.dk/ase/ase/atoms.html#ase.atoms.Atoms.center
>
>   This center function does not really solve my problem. I will try out
> the stuff
> which Gael is proposing.
>
>  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.
>
> With 'order' I mean not the order of the atoms, of course. - I don't
> want to destroy the structure which I got from heavy calculations. ;-)
> I merely meant to re-arrange atoms (translation with cell vectors)
> in the cell such that they are all together, in the center of the cell.
>
> Thanks for help,
>
> CB.
>
>
>
> 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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>>
>> ----------------------------------------------------------------------
>>
>> 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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