From: Decai Yu (decai-yu_at_northwestern.edu)
Date: Fri Feb 12 2010 - 15:20:16 CST

Axel,

Thanks.
The cell is not orthorhombic.
The CHGCAR includes the cell vector and the fractional coordinates.
While the xyz file is directly converted from CHGCAR to Cartesian
coordinates.
How can I do the same transformation of xyz coordinates?

Decai
 
 

> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Friday, February 12, 2010 3:01 PM
> To: Decai Yu
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: xyz file and VASP CHGCAR file do not overlap
>
> 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
> >
> >
> >
> >
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.