From: Tyler Smith (tylersmith2_at_mail.usf.edu)
Date: Fri Jan 03 2014 - 19:02:57 CST

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>
>
>
>