VMD-L Mailing List

From: Decai Yu (decai-yu_at_northwestern.edu)
Date: Mon Feb 15 2010 - 10:26:46 CST

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.

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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