VMD-L Mailing List

From: Decai Yu (decai-yu_at_northwestern.edu)
Date: Wed Feb 17 2010 - 11:23:56 CST

Axel and Matt,

Thanks for the help and suggestions.
I figured out a way to get around this.
Instead of loading xyz, I can load either OUTCAR or vasprun.xml to get
the correct element types and xyz coordinates.

Decai

 

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
Behalf
> Of Axel Kohlmeyer
> Sent: Monday, February 15, 2010 11:22 AM
> To: Decai Yu
> Cc: matt watkins; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: xyz file and VASP CHGCAR file do not overlap
>
> 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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http://www.opera.com/mail/
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.