VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 26 2010 - 16:11:41 CST

On Fri, Nov 26, 2010 at 8:37 AM, Germain Salvato Vallverdu
<germain.vallverdu_at_univ-pau.fr> wrote:
> Axel

germain,

please always keep the list in cc: so that others can
see how your problems are resolved.

thanks.

>
> Thanks for your answer. I agree with you, all you need is in the POSCAR
> but I do not know how can I say to VMD to read that data !

i don't understand your question.

if you read a POSCAR file, vmd should read what is there.

i don't know/use VASP, but from reading the source for the
vasp poscar plugin, it is evident, that it will read and send
system cell information to VMD.

there is no additional command needed.

> Do you know how to do this ?

you have to explain in more detail what steps _exactly_ you
are doing and how you determine that something has yet to be
transferred from the VASP file to VMD.

axel.

>
> Thanks
>
> Germain
>
> -------- Message initial --------
> De: Axel Kohlmeyer <akohlmey_at_gmail.com>
> : Germain Salvato Vallverdu <germain.vallverdu_at_univ-pau.fr>
> Cc: vmd-l_at_ks.uiuc.edu
> Sujet: Re: vmd-l: VASP crystal structure visualisation
> Date: Thu, 25 Nov 2010 18:10:04 -0500
>
> On Thu, Nov 25, 2010 at 7:41 AM, Germain Salvato Vallverdu
> <germain.vallverdu_at_univ-pau.fr> wrote:
>> Hi all,
>>
>> I would like to visualise CONTCAR or POSCAR file with VMD. I can do that
>> because that format are available in VMD thanks to the vasp plugin. But
>> I would like to draw the cell edge of the crystal.
>>
>> From the pbc plugins I tried that commands :
>>
>> pbc set {5.7 5.7 5.7} -all
>
> why do you set the box? the
> POSCAR reader should read it from the file.
>
> as for the location of the box, you can set the position
> for the box with a command line option to pbc box.
> (-center ?)
>
> for details see the online documentation
>
> axel
>
>> pbc box -color red -style tubes -width 1
>>
>> That draw a nice box but how can I control the position of the box ? For
>> exemple I would like to set one corner of the box to the origin or to
>> the coordinate of the atom at the origin.
>>
>> Second question, what about non ortorhombic cell ?
>>
>> Thanks for your help
>>
>> Germain
>>
>>
>> --
>> Matre de Confrence
>> Universit de Pau et des pays de l'Adour
>> IPREM - ECP - CTR
>> germain.vallverdu_at_univ-pau.fr
>> 05 59 40 78 51
>> http://germain-salvato-vallverdu.blogspot.com/
>>
>>
>
>
>
>
> --
> Matre de Confrence
> Universit de Pau et des pays de l'Adour
> IPREM - ECP - CTR
> germain.vallverdu_at_univ-pau.fr
> 05 59 40 78 51
> http://germain-salvato-vallverdu.blogspot.com/
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.