• ## Outreach

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sun Nov 30 2014 - 20:30:50 CST

A simple workaround is to use the volmult tool from Situs. If you multiply your non-orthorhombic map by an orthorhombic map (for example, one produced using volmap mask in VMD), the output will be orthorhombic.

Cheers,

Tristan

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Miguel Caro
Sent: Saturday, 29 November 2014 2:01 AM
To: Axel Kohlmeyer
Cc: Vmd l
Subject: Re: vmd-l: How to make solid surfaces work with non-orthorhombic cells

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><mailto: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<mailto:mcaroba_at_gmail.com>

Work: miguel.caro_at_aalto.fi<mailto: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<mailto:mcaroba_at_gmail.com>
Work: miguel.caro_at_aalto.fi<mailto:miguel.caro_at_aalto.fi>
Website: http://mcaroba.dyndns.org