VMD-L Mailing List

From: Miguel Caro (miguel.caro_at_aalto.fi)
Date: Fri Nov 28 2014 - 10:00:59 CST

Hi Axel, thanks for the reply.

After you suggested to look at xsf I actually converted the VASP file to
xsf and I run against into the same problem: points are fine but
surfaces are not.

I do not know how VMD works internally so this might be a stupid
question: could it be that VMD does not like data provided in a
non-orthorhombic grid when drawing the surfaces? That is, not only the
lattice is (in my case) hexagonal, but also the grid where the charge
density is given.

If the solution is too complicated I can always write a script to
convert to an orthorhombic grid through interpolation.

Many thanks,
Miguel

On 2014-11-28 15:04, Axel Kohlmeyer wrote:
> On Fri, Nov 28, 2014 at 5:02 AM, Miguel Caro <miguel.caro_at_aalto.fi> wrote:
>> Hi all,
>>
>> I'm trying to plot some charge density isosurfaces importing the data using
>> VASP's PARCHG file format. When the unit cell is not orthorhombic the "Solid
>> Surface" Draw style does not work properly (VMD seems to interpret the
>> lattice vectors as belonging to an orthorhombic lattice), whereas "Points"
>> works fine. For orthorhombic cells both Draw styles work fine. Is there a
>> work around this issue? My VMD version is 1.9.1.
> you are most likely running into a limitation of the molfile plugin
> for these files.
> the solution would be to improve the plugin. you can look at the
> plugins for cube or xsf files for examples how to handle
> non-orthogonal cells.
>
> axel.
>
>> Thanks,
>> Miguel
>> --
>> Dr. Miguel Caro
>> Postdoctoral researcher
>> Department of Electrical Engineering and Automation,
>> and COMP Centre of Excellence in Computational Nanoscience
>> Aalto University, Finland
>> Personal email: mcaroba_at_gmail.com
>> Work: miguel.caro_at_aalto.fi
>> Website: http://mcaroba.dyndns.org
>
> 

-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba_at_gmail.com*
Work: *miguel.caro_at_aalto.fi*
Website: http://mcaroba.dyndns.org