VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Nov 28 2014 - 05:49:09 CST

I guess no easy one. Have a look at:

 

 <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

 

Where there is written:

 

Unit Cell
All files are assumed to have an orthogonal unit cell.

 

And I assume that your data is treated as 3D scalar grid data. This also means that using the points representation can actually not work, too, but might be less obvious. I think you could emulate a orthorhombic box which can hold your non orthorhombic one and convert your data.

 

Or can you supply a picture of what you currently get when you try to show the isosurface?

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Miguel Caro
Gesendet: Freitag, 28. November 2014 11:03
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: How to make solid surfaces work with non-orthorhombic cells

 

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.

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