VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 14 2014 - 09:50:05 CST

Tyler,
  Did you get your problem resolved?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 03, 2014 at 09:04:28PM -0600, John Stone wrote:
> 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/ 

-- 
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/