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