From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 15 2010 - 11:22:28 CST

On Mon, Feb 15, 2010 at 11:26 AM, Decai Yu <decai-yu_at_northwestern.edu> wrote:
> Matt,
>
> Thanks.
> It worked fine for CHGCAR AND POSCAR.
> But the problem with POSCAR is that it does not show element types.
> That is why I chose to load xyz file instead of POSCAR, which created
> the problem.

you should be able to work around this.
load the .xyz and write out a .psf file.
then load the POSCAR and the .psf file
(you have to check which order is better)
and then the CHGCAR.
this way you can set the element labels
(and bonds) explicitly in the .psf and
then just add coordinates to it.

cheers,
   axel.

>
> Decai
>
>
>
>> -----Original Message-----
>> From: matt watkins [mailto:ucapmw0_at_ucl.ac.uk]
>> Sent: Friday, February 12, 2010 7:54 PM
>> To: Axel Kohlmeyer; Decai Yu
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: xyz file and VASP CHGCAR file do not overlap
>>
>> Hi,
>>
>> what version of VMD are you using?  I think that 1.8.7 should load
> POSCAR
>> ( or CONTCAR) and CHGCAR consistently. At least for hexagonal cells it
>> worked correctly for me.
>>
>> Matt
>>
>> On Sat, 13 Feb 2010 06:00:45 +0900, Axel Kohlmeyer
> <akohlmey_at_gmail.com>
>> wrote:
>>
>> > On Fri, 2010-02-12 at 13:29 -0600, Decai Yu wrote:
>> >> Dear All,
>> >>
>> >>
>> >>
>> >> I am trying to load VASP CHGCAR and xyz file together to VMD.
>> >>
>> >> The xyz file is converted from CHGCAR.
>> >>
>> >> However, it seems that charge density and atoms in xyz file do not
>> >> overlap.
>> >>
>> >> How can I solve this problem?
>> >
>> > i don't anything about VASP, or the corresponding plugins,
>> > but could it be that your system is not orthorhombic?
>> >
>> > in that case, the density is most likely rotated
>> > for proper PBC display and you'd have to use the
>> > same transformation on the coordinates. do you
>> > have the coordinates in a different format? one
>> > that has the cell included...
>> >
>> >
>> > axel.
>> >
>> >>
>> >> You help is appreciated.
>> >>
>> >>
>> >>
>> >> Regards,
>> >>
>> >>
>> >>
>> >> Decai Yu
>> >>
>> >> Northwestern University
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >
>>
>>
>> --
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>
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.