VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 25 2021 - 23:59:30 CST

Hi,
  One way to ensure that the .vmdrc and scripts don't interfere with
each other is to use commands via "after idle".

If the actual Tachyon rendering is freezing, this may indicate an issue
arising from the more limited floating point coordinate precision used in
the .dat scene files, whereas the built-in "TachyonInternal" renderer that
operates inside of VMD will not be translated from binary to decimal and
back again. This might matter if one has scenes with nearly coplanar
surfaces that are close to touching, with either transparent or reflective
surfaces.

It would help to have more details here.
What happens if the script is changed to use "TachyonInternal" instead of
"Tachyon"?

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jan 18, 2021 at 02:41:44PM +0000, Vermaas, Josh wrote:
> My understanding of the tachyon renderer is that it generates an input
> file for tachyon, which can then be run totally independently from VMD. It
> is an important distinction if VMD is failing to write the input file, or
> if tachyon is failing to render the input file. What happens if you use
> TachyonInternal? Then you don't have to do the handoff. I've also had
> issues in the past when I rendered from a script, as sometimes elements
> from a .vmdrc are run after the script itself is, which would lead to
> things looking different than how you expected (including black screens).
>
>
>
> -Josh
>
>
>
> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Soumik Ghosh
> <soumik2805_at_gmail.com>
> Date: Sunday, January 17, 2021 at 12:53 PM
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: Tachyon sometimes suddenly freezes up when rendering
> epotential images
>
>
>
> Hi,
>
>
>
> I have been trying to create Tachyon eoptential figures using vmd. When I
> render it manually via the GUI it works, but when I try to render these
> figures via a script, sometimes the rendering gets stuck at some %
> completion. it results in incomplete rendered pictures and sometimes I
> have to manually kill it. Can you please help? Following is the script I
> use.
>
> -------------
>
> display depthcue off
> display projection Orthographic
>
>
>
> mol addfile epotential.dx type dx first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
>
> mol addfile density.dx type dx first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
>
>
>
> mol delrep 0 top
> mol representation Isosurface 0.000100 1 0 0 1 1
> mol color Volume 0
> mol selection {all}
> mol material Opaque
> mol addrep top
> mol selupdate 0 top 0
> mol colupdate 0 top 0
> mol scaleminmax top 0 -0.080000 0.080000
> mol smoothrep top 0 0
>
>
>
> display resetview
> scale by 0.7
> drawframes top 0 {0:2}
> color Display Background white
> axes location Off
> material change specular Transparent 0.220000
> material change shininess Transparent 0.660000
> material change opacity Transparent 0.300000
>
>
>
> render Tachyon VMDscene.dat "/usr/bin/tachyon" -aasamples 12 %s -format
> TARGA -o %s_rot0.tga
>
> rotate {x} by 90
>
> render Tachyon VMDscene.dat "/usr/bin/tachyon" -aasamples 12 %s -format
> TARGA -o %s_rotx.tga
>
> rotate {x} by -90
>
> rotate {y} by 90
>
> render Tachyon VMDscene.dat "/usr/bin/tachyon" -aasamples 12 %s -format
> TARGA -o %s_roty.tga
>
> ------------
>
>
>
> Thanking you in advance,
>
> Soumik Ghosh
>
> --
>
> Soumik Ghosh
> Marie Skl/odowska-Curie Fellow
>
> SciClus GmbH & Co. KG
> Moritz-von-Rohr-Str. 1a
> 07745 Jena
>
> Tel +49 3641/27893 33
> Fax +49 3641/27893 99
> [1]www.sciclus.de
>
> Unternehmenssitz: Jena
> Handelsregister: Jena HRA 504364
>
> Persönlich haftende Gesellschafterin:
> SciClus Administration GmbH - Sitz: Jena
> Handelsregister: Jena HRB 513216
> Geschäftsführer: Dr. Burkhard Jahn, Dr. Martin Presselt
>
> [2]www.logiclab-itn.eu
>
> Follow us on Twitter:
> [3]twitter.com/Leibniz_IPHT
> [4]twitter.com/LogicLab_ITN
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__http:/www.sciclus.de/__;!!DZ3fjg!uzRsIDopW-ZG8ocqMJkKtKf3J07qPpOOZ5gdDbNhgGHONivClcmZM8EYngorQ-VH8A$
> 2. https://urldefense.com/v3/__http:/www.logiclab-itn.eu/__;!!DZ3fjg!uzRsIDopW-ZG8ocqMJkKtKf3J07qPpOOZ5gdDbNhgGHONivClcmZM8EYngpyJG36Fw$
> 3. https://urldefense.com/v3/__http:/twitter.com/Leibniz_IPHT__;!!DZ3fjg!uzRsIDopW-ZG8ocqMJkKtKf3J07qPpOOZ5gdDbNhgGHONivClcmZM8EYngrqdR3tyA$
> 4. https://urldefense.com/v3/__http:/twitter.com/LogicLab_ITN__;!!DZ3fjg!uzRsIDopW-ZG8ocqMJkKtKf3J07qPpOOZ5gdDbNhgGHONivClcmZM8EYngoDsCrFmA$ 

-- 
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/