VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 04 2014 - 10:33:04 CST

Axel, Olaf,
  Ah, okay, that explains the missing code in the new version.
Olaf, if it's not too much trouble for you, it would be nice to
re-incorporate Axel's ~24 line diff into your latest version as well.

Cheers,
  John

On Tue, Feb 04, 2014 at 11:29:13AM -0500, Axel Kohlmeyer wrote:
> On Tue, Feb 4, 2014 at 11:21 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Hi Olaf,
> > I have committed your new VTF plugin to the VMD CVS.
> > I noticed that your new version no longer has the #ifdef to allow
> > the Tcl-related features to be disabled. This is fine, but the end
>
> john,
>
> that change was added by me to make the plugin compatible with the
> standalone catdcd windows installer, for which Tcl support doesn't
> make much sense. i think i had sent an e-mail to olaf about this, but
> i am not certain. from cvs log:
>
> ----------------------------
> revision 1.16
> date: 2013/07/20 14:38:12; author: akohlmey; state: Exp; lines: +22 -2
> allow compilation of VTF plugin without Tcl using -DVTF_DISABLE_TCL
> ----------------------------
>
> axel.
>
> > result is that your plugin will now only be compiled when calling progs
> > have been linked with Tcl (e.g. likely not as part of tools other
> > than VMD, e.g. Pymol, Gromacs, etc., which use the VMD plugins but
> > usually don't link against Tcl, at least to my knowledge)
> > If you want to preserve the ability for the VTF plugin to be used with
> > tools other than VMD, you might consider adding that #ifdef back in.
> > Either way is fine with me, I just wanted to mention that the VMD
> > molfile plugins have started to get used with other packages too...
> >
> > Cheers,
> > John
> >
> > On Tue, Feb 04, 2014 at 03:32:49PM +0100, Olaf Lenz wrote:
> >> Hi everybody!
> >> Sorry if you get this mailing twice. In the last mailing, I have attached
> >> a DLL file, which caused the mailing to be banned by some systems.
> >> After I have found out that Microsoft does actually have a free compiler
> >> version, I have taken the time to set up a devel environment in windows,
> >> and I have set out to debug the code. The problem was that sscanf does not
> >> really work the same in Windows and Unix, at least when "%n" is involved.
> >> I have fixed the problem, and furthermore I have learned how to use Visual
> >> C++ and how to compile a DLL. I have tested the plugin with VMD on
> >> Windows, and I was able to open your sample file and others that failed as
> >> well.
> >> AtA
> >> A https://github.com/olenz/vtfplugin/releases/tag/wintest
> >> you can get the dynamic library and its source code. Put the DLL into some
> >> directory on your machine and useA
> >> A vmd_plugin_scandirectory <dir> *.dll
> >> in vmd.rc to load it. Ming-Tsung, would you please test whether the plugin
> >> works for you as well?
> >> John, I would be happy if you would add the updated plugin to the VMD
> >> repo.
> >> Olaf
> >>
> >> 2014-02-04 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> >>
> >> hi,
> >>
> >> here is a binary for win32 cross-compiled from the unmodified latest
> >> vtfplugin sources on linux. this version does not support the Tcl
> >> functions and transparent gzip decompression. please uncompress it,
> >> make a backup copy of the original and replace it with this file and
> >> give it a try.
> >> axel.
> >> On Mon, Feb 3, 2014 at 5:36 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> > Hi guys,
> >> > A Most likely this is an issue with uninitialized data, a buffer
> >> overrun,
> >> > or something similar. A Have you done tests with the failing input
> >> using
> >> > valgrind on Linux? A If not, I'd try that first. A If that works out
> >> fine,
> >> > then it's possible we're dealing with something that is indeed
> >> specific
> >> > to Windows, but most things that fail on Windows will also show up in
> >> > testing under Linux if one makes careful use of valgrind etc. A I will
> >> > soon be making test builds of VMD 1.9.2 beta versions on Windows, so
> >> it
> >> > will be easier to track down anything that is truly unique to Windows
> >> > once I have those builds prepared.
> >> >
> >> > Cheers,
> >> > A John
> >> >
> >> > On Mon, Feb 03, 2014 at 07:09:13PM +0100, Olaf Lenz wrote:
> >> >> A A Hi!
> >> >>
> >> >> A A The trouble is that I do not have access to a Windows
> >> development system.
> >> >> A A With your message, I can have a look at the code again, but I am
> >> unable to
> >> >> A A compile or debug under Windows.
> >> >>
> >> >> A A Olaf
> >> >>
> >> >> A A Dr. rer. nat. Olaf Lenz
> >> >> A A Institut fA 1/4r Computerphysik, Allmandring 3, D-70569
> >> Stuttgart
> >> >> A A Phone: +49.711.685.63607
> >> >>
> >> >> A A Am 03.02.2014 18:51 schrieb "Ming-Tsung Lee"
> >> <mtlee_at_rci.rutgers.edu>:
> >> >>
> >> >> A A A Hi Olaf,
> >> >> A A
> >> A http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22262.html
> >> >> A A A I think that I probably find the bug. In the VTF file
> >> generated by
> >> >> A A A DL_MESO (attached, not sure the situation of ESPresSo). In
> >> the first
> >> >> A A A frame of the trajectory, box dimensions are defined as
> >> follows
> >> >> A A A timestep indexed
> >> >> A A A pbc A 15.000000 15.000000 15.000000
> >> >> A A A A A A A A A A 0 10.867398 12.150888 14.039090
> >> >> A A A A A A A A A A 1 A 9.467130 10.474655 12.615115
> >> >> A A A A A A A A A A 2 A ...
> >> >> A A A I have checked the default syntax of VTF. The box angles
> >> should be
> >> >> A A A optional.
> >> >> A A A https://github.com/olenz/vtfplugin/wiki/VTF-format
> >> >> A A A I have played that around. It looks like that VMD is frozen
> >> while
> >> >> A A A loading the line pbc/unitcell, as long as there are no "90 90
> >> 90"
> >> >> A A A assigned. Nevertheless, the same VTF works perfectly well
> >> with the Linux
> >> >> A A A version VMD. Would you please check your plugins for both
> >> platforms?
> >> >> A A A Probably something is messed up in the Windows version. Thank
> >> you.
> >> >> A A A For those who are using DL_MESO and want a quick solution for
> >> this,
> >> >> A A A simply modify the trajectory output by putting a "90 90 90"
> >> after your
> >> >> A A A box dimensions. It will work.
> >> >> A A A Best,
> >> >> A A A MT
> >> >> A A A P.S. I am using Windows 7 x64 enterprise, VMD 1.9.1.
> >> Trajectory is
> >> >> A A A generated from DL_MESO/DEMO/Polyelectrolyte/HISTORY, using
> >> >> A A A /DL_MESO/DPD/utility/trajectselected.f90A
> >> >> A A A Ming-Tsung Lee
> >> >> A A A Department of Chemical & Biochemical Engineering
> >> >> A A A Rutgers, The State University of New Jersey
> >> >> A A A 98 Brett Road
> >> >> A A A Piscataway, NJ 08854
> >> >> A A A tel: 848-445-6953
> >> >
> >> > --
> >> > 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/ A A A A A Phone: 217-244-3349
> >> > http://www.ks.uiuc.edu/Research/vmd/
> >>
> >> --
> >> Dr. Axel Kohlmeyer A akohlmey_at_gmail.com A http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >>
> >> --
> >> Dr. rer. nat. Olaf Lenz
> >> Institut fA 1/4r Computerphysik, Allmandring 3, D-70569 Stuttgart
> >> Phone: +49-711-685-63607
> >
> > --
> > 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/
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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/