VMD-L Mailing List
From: Caro Miguel (miguel.caro_at_aalto.fi)
Date: Mon Dec 01 2014 - 10:57:05 CST
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Thanks John,
This indeed resolved the issue. VMD 1.9.2 also seems to run better on my machine in general.
Thanks again,
Miguel
Dr. Miguel Caro
Postdoctoral researcher
Department of Electrical Engineering and Automation, and
COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Email: mcaroba_at_gmail.com
Work: miguel.caro_at_aalto.fi
Website: http://mcaroba.dyndns.org
________________________________________
From: John Stone [johns_at_ks.uiuc.edu]
Sent: 29 November 2014 01:28
To: Caro Miguel
Cc: Axel Kohlmeyer; Vmd l
Subject: Re: vmd-l: How to make solid surfaces work with non-orthorhombic cells
Hi,
There was a bug in VMD 1.9.1 with regard to display of isosurfaces
in non-orthorhombic unit cells, but this has been fixed in the
VMD 1.9.2 test builds that are available on the web site. Please test
the new VMD 1.9.2 beta version, and that should cure your problem.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Fri, Nov 28, 2014 at 06:00:59PM +0200, Miguel Caro wrote:
> 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 [1]<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: [2]mcaroba_at_gmail.com
> Work: [3]miguel.caro_at_aalto.fi
> Website: [4]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: [5]mcaroba_at_gmail.com
> Work: [6]miguel.caro_at_aalto.fi
> Website: [7]http://mcaroba.dyndns.org
>
> References
>
> Visible links
> 1. mailto:miguel.caro_at_aalto.fi
> 2. mailto:mcaroba_at_gmail.com
> 3. mailto:miguel.caro_at_aalto.fi
> 4. http://mcaroba.dyndns.org/
> 5. mailto:mcaroba_at_gmail.com
> 6. mailto:miguel.caro_at_aalto.fi
> 7. http://mcaroba.dyndns.org/
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: Anjela Manandhar: "Re: GTP and GDP parameter files"
- Previous message: Kshatresh Dutta Dubey: "paratool/forcefield tool error"
- In reply to: John Stone: "Re: How to make solid surfaces work with non-orthorhombic cells"
- Next in thread: Tristan Croll: "RE: How to make solid surfaces work with non-orthorhombic cells"
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