VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 03 2014 - 21:04:28 CST

Tyler,
  I'm out of the office this week, so I didn't get to your emails
until just now. Josh's suggestion is the most likely solution to
any cases where you see differences between the output of a ray tracer
and that of OpenGL ("snapshot"). When you have multiple spheres of
identical radii and identical coordinate, the ray tracer and OpenGL
can end up drawing different ones as being visible, depending on their
order in the list of primitives to be drawn. This is not specific just
to Tachyon, but is similar for other renderers as well. The solution as
Josh already suggested, is to avoid drawing identical sized concentric
spheres with different colors...

Cheers,
  John Stone

On Fri, Jan 03, 2014 at 08:02:57PM -0500, Tyler Smith wrote:
> Hi Ryan,
> I'm embarrassed to tell you I don't know what you mean by a precompiled
> binary, so I can't be of much help on that front. Just out of curiosity
> were you able to get multiple frames colored correctly with Tachyon
> Internal or just one? I should probably clarify that when I attempt to
> render multiple frames with Tachyon Internal it's not that some of the
> monomers are the wrong shade; for many of the frames all the atoms will be
> one color. As Dr. Hoy said, if you'd like to see the PSF/PDB files we're
> using or anything else you think might be relevant don't hesitate to ask.
> Thanks,
>
> Tyler
>
> On Fri, Jan 3, 2014 at 5:43 PM, Ryan Hoffman <rmhoff_at_scripps.edu> wrote:
>
> I get similar colors comparing TachyonInternal (.bmp) and Snapshot
> (.tga). I didn't exactly reproduce your workflow though -- I didn't run
> a separate script to get the snapshot. Maybe Josh's suggestion (not
> superimposing two spheres) will help.
>
> ry
>
> ________________________________________
> From: Hoy, Robert [rshoy_at_usf.edu]
> Sent: Friday, January 03, 2014 14:45
> To: Ryan Hoffman
> Cc: Smith, Tyler; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Issues with tachyon internal renderer
>
> Hi again, Ryan. Ah, OK, I didn't know ray tracers had this feature.
> Yep, certainly it could be some other error, or a bug - one can never
> rule that out though we've tried pretty hard to.
>
> We have duplicated this issue on both a Mac and a Linux box running
> CentOS, so I don't think it's an OS or graphics-card issue.
>
> I believe the binaries were precompiled, but am not sure --- Tyler?
>
> Thanks,
> Rob
>
> Robert Hoy
> Assistant Professor of Physics
> University of South Florida
> 813-974-0063
>
> On Jan 3, 2014, at 5:32 PM, Ryan Hoffman
> <rmhoff_at_scripps.edu<mailto:rmhoff_at_scripps.edu>> wrote:
>
> My understanding about ray tracers in general is that the resulting
> colors are due to interactions between 'material' and 'lighting'
> settings. So a red apple under a green light source looks black. But
> maybe this is some other kind of user error, or maybe even a bug.
>
> What system is this on? Were the binaries pre-compiled?
>
> I'll play for a few more minutes and get back to you.
>
> ry
> ________________________________________
> From: Hoy, Robert [rshoy_at_usf.edu<mailto:rshoy_at_usf.edu>]
> Sent: Friday, January 03, 2014 14:27
> To: Smith, Tyler
> Cc: Ryan Hoffman; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Issues with tachyon internal renderer
>
> Hi, Ryan. It's not a lighting issue -- the colors are completely
> different, and "right" in Snapshot" but "wrong" in Tachyon. Besides the
> TCL scripts, would you also like us to send you some PSF/PDB files, or
> anything else?
>
> Thanks a lot for your help!
>
> Rob
>
> Robert Hoy
> Assistant Professor of Physics
> University of South Florida
> 813-974-0063
>
> On Jan 3, 2014, at 5:24 PM, Tyler Smith
> <tylersmith2_at_mail.usf.edu<mailto:tylersmith2_at_mail.usf.edu><mailto:tylersmith2_at_mail.usf.edu>>
> wrote:
>
> sure
>
> On Fri, Jan 3, 2014 at 5:07 PM, Ryan Hoffman
> <rmhoff_at_scripps.edu<mailto:rmhoff_at_scripps.edu><mailto:rmhoff_at_scripps.edu>>
> wrote:
> Can we see some of the resulting Tcl script? Maybe a lighting issue?
> ry
> ________________________________________
> From:
> owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu><mailto:owner-vmd-l_at_ks.uiuc.edu>
> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu><mailto:owner-vmd-l_at_ks.uiuc.edu>]
> On Behalf Of Tyler Smith
> [tylersmith2_at_mail.usf.edu<mailto:tylersmith2_at_mail.usf.edu><mailto:tylersmith2_at_mail.usf.edu>]
> Sent: Friday, January 03, 2014 12:19
> To:
> vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
> Cc: Robert Hoy
> Subject: vmd-l: Issues with tachyon internal renderer
>
> Hi All,
> I'm attempting to create a movie in vmd that shows how the local
> crystallization of a system of polymers evolves with time during
> quenching. A metric for local crystallization called the CCE norm was
> used to assign every monomer in the system a crystalline structure (
> HCP, FCC, fivefold, unordered). Psf files were used to convey
> information about the crystalline structure using dummy variables; for
> example, all monomers with mass < .2 correspond to monomers with FCC
> ordering and are colored red. Every psf file gives local crystalline
> structure for one timestep in the quench, so in order to create a movie
> of evolving crystalline structure a new pair of psf and pdb files needs
> to be loaded in for every frame. As far as i know vmd can't internally
> create movies with multiple psf files, so I decided to render a series
> of bitmap images using vmd and then string them together using another
> program.
>
> A c++ program was used to create a long .tcl script that loads in
> the pdb and modified psf, colors the monomers accordingly, renders an
> image and then repeats for the next pair of files. This process worked
> well using the snapshot renderer, but I would prefer to generate higher
> quality images using Tachyon Internal. When the Tachyon Internal
> renderer is employed images are rendered but they are not colored
> correctly.
>
> Does anyone have any ideas as to why snapshot works and TachyonInternal
> doesn't? I'll attach the c++ scripts used to generate the .tcl scripts
>
> Also if there is an easier way to create movies with multiple psf
> files and custom coloring please let me know.
>
> Thanks,
>
> Tyler
>
> ________________________________
>
> <snapshot.tcl><TachyonInternal.tcl> 

-- 
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/