VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 04 2014 - 11:01:47 CST

Okay, I have committed the latest version you sent to the VMD CVS.
It'll show up on the public read-only CVS later tonight, and it'll
be in the next round of VMD test builds I do.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 04, 2014 at 05:57:10PM +0100, Olaf Lenz wrote:
> Gosh, good that this error turned up. I have accidentally sent you an even
> older version of the plugin, as I had done the development on another
> branch...
> Attached, find my latest version. This one actually contains the fixes for
> Windows, and also the TCL-defines that I introduced only today.
> Olaf
>
> 2014-02-04 John Stone <johns_at_ks.uiuc.edu>:
>
> Axel, Olaf,
> A 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,
> A 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,
> > > A 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. A 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; A author: akohlmey; A state: Exp; A 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,
> > > A John
> > >
> > > On Tue, Feb 04, 2014 at 03:32:49PM +0100, Olaf Lenz wrote:
> > >> A A Hi everybody!
> > >> A A Sorry if you get this mailing twice. In the last mailing, I
> have attached
> > >> A A a DLL file, which caused the mailing to be banned by some
> systems.
> > >> A A After I have found out that Microsoft does actually have a
> free compiler
> > >> A A version, I have taken the time to set up a devel environment
> in windows,
> > >> A A and I have set out to debug the code. The problem was that
> sscanf does not
> > >> A A really work the same in Windows and Unix, at least when "%n"
> is involved.
> > >> A A I have fixed the problem, and furthermore I have learned how
> to use Visual
> > >> A A C++ and how to compile a DLL. I have tested the plugin with
> VMD on
> > >> A A Windows, and I was able to open your sample file and others
> that failed as
> > >> A A well.
> > >> A A AtA
> > >> A A A A https://github.com/olenz/vtfplugin/releases/tag/wintest
> > >> A A you can get the dynamic library and its source code. Put the
> DLL into some
> > >> A A directory on your machine and useA
> > >> A A A A vmd_plugin_scandirectory <dir> *.dll
> > >> A A in vmd.rc to load it. Ming-Tsung, would you please test
> whether the plugin
> > >> A A works for you as well?
> > >> A A John, I would be happy if you would add the updated plugin to
> the VMD
> > >> A A repo.
> > >> A A Olaf
> > >>
> > >> A A 2014-02-04 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> > >>
> > >> A A A hi,
> > >>
> > >> A A A here is a binary for win32 cross-compiled from the
> unmodified latest
> > >> A A A vtfplugin sources on linux. this version does not support
> the Tcl
> > >> A A A functions and transparent gzip decompression. please
> uncompress it,
> > >> A A A make a backup copy of the original and replace it with this
> file and
> > >> A A A give it a try.
> > >> A A A axel.
> > >> A A A On Mon, Feb 3, 2014 at 5:36 PM, John Stone
> <johns_at_ks.uiuc.edu> wrote:
> > >> A A A > Hi guys,
> > >> A A A > A A Most likely this is an issue with uninitialized data,
> a buffer
> > >> A A A overrun,
> > >> A A A > or something similar. A Have you done tests with the
> failing input
> > >> A A A using
> > >> A A A > valgrind on Linux? A If not, I'd try that first. A If
> that works out
> > >> A A A fine,
> > >> A A A > then it's possible we're dealing with something that is
> indeed
> > >> A A A specific
> > >> A A A > to Windows, but most things that fail on Windows will
> also show up in
> > >> A A A > testing under Linux if one makes careful use of valgrind
> etc. A I will
> > >> A A A > soon be making test builds of VMD 1.9.2 beta versions on
> Windows, so
> > >> A A A it
> > >> A A A > will be easier to track down anything that is truly
> unique to Windows
> > >> A A A > once I have those builds prepared.
> > >> A A A >
> > >> A A A > Cheers,
> > >> A A A > A A John
> > >> A A A >
> > >> A A A > On Mon, Feb 03, 2014 at 07:09:13PM +0100, Olaf Lenz
> wrote:
> > >> A A A >> A A A Hi!
> > >> A A A >>
> > >> A A A >> A A A The trouble is that I do not have access to a
> Windows
> > >> A A A development system.
> > >> A A A >> A A A With your message, I can have a look at the code
> again, but I am
> > >> A A A unable to
> > >> A A A >> A A A compile or debug under Windows.
> > >> A A A >>
> > >> A A A >> A A A Olaf
> > >> A A A >>
> > >> A A A >> A A A Dr. rer. nat. Olaf Lenz
> > >> A A A >> A A A Institut fA 1/4r Computerphysik, Allmandring 3,
> D-70569
> > >> A A A Stuttgart
> > >> A A A >> A A A Phone: +49.711.685.63607
> > >> A A A >>
> > >> A A A >> A A A Am 03.02.2014 18:51 schrieb "Ming-Tsung Lee"
> > >> A A A <mtlee_at_rci.rutgers.edu>:
> > >> A A A >>
> > >> A A A >> A A A A A Hi Olaf,
> > >> A A A >> A A A
> > >> A A A A
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22262.html
> > >> A A A >> A A A A A I think that I probably find the bug. In the
> VTF file
> > >> A A A generated by
> > >> A A A >> A A A A A DL_MESO (attached, not sure the situation of
> ESPresSo). In
> > >> A A A the first
> > >> A A A >> A A A A A frame of the trajectory, box dimensions are
> defined as
> > >> A A A follows
> > >> A A A >> A A A A A timestep indexed
> > >> A A A >> A A A A A pbc A 15.000000 15.000000 15.000000
> > >> A A A >> A A 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 A A A A A 1 A 9.467130 10.474655 12.615115
> > >> A A A >> A A A A A A A A A A A A 2 A ...
> > >> A A A >> A A A A A I have checked the default syntax of VTF. The
> box angles
> > >> A A A should be
> > >> A A A >> A A A A A optional.
> > >> A A A >> A A A A A
> https://github.com/olenz/vtfplugin/wiki/VTF-format
> > >> A A A >> A A A A A I have played that around. It looks like that
> VMD is frozen
> > >> A A A while
> > >> A A A >> A A A A A loading the line pbc/unitcell, as long as
> there are no "90 90
> > >> A A A 90"
> > >> A A A >> A A A A A assigned. Nevertheless, the same VTF works
> perfectly well
> > >> A A A with the Linux
> > >> A A A >> A A A A A version VMD. Would you please check your
> plugins for both
> > >> A A A platforms?
> > >> A A A >> A A A A A Probably something is messed up in the Windows
> version. Thank
> > >> A A A you.
> > >> A A A >> A A A A A For those who are using DL_MESO and want a
> quick solution for
> > >> A A A this,
> > >> A A A >> A A A A A simply modify the trajectory output by putting
> a "90 90 90"
> > >> A A A after your
> > >> A A A >> A A A A A box dimensions. It will work.
> > >> A A A >> A A A A A Best,
> > >> A A A >> A A A A A MT
> > >> A A A >> A A A A A P.S. I am using Windows 7 x64 enterprise, VMD
> 1.9.1.
> > >> A A A Trajectory is
> > >> A A A >> A A A A A generated from
> DL_MESO/DEMO/Polyelectrolyte/HISTORY, using
> > >> A A A >> A A A A A /DL_MESO/DPD/utility/trajectselected.f90A
> > >> A A A >> A A A A A Ming-Tsung Lee
> > >> A A A >> A A A A A Department of Chemical & Biochemical
> Engineering
> > >> A A A >> A A A A A Rutgers, The State University of New Jersey
> > >> A A A >> A A A A A 98 Brett Road
> > >> A A A >> A A A A A Piscataway, NJ 08854
> > >> A A A >> A A A A A tel: 848-445-6953
> > >> A A A >
> > >> A A A > --
> > >> A A A > NIH Center for Macromolecular Modeling and Bioinformatics
> > >> A A A > Beckman Institute for Advanced Science and Technology
> > >> A A A > University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> > >> A A A > http://www.ks.uiuc.edu/~johns/ A A A A A A A A A A Phone:
> 217-244-3349
> > >> A A A > http://www.ks.uiuc.edu/Research/vmd/
> > >>
> > >> A A A --
> > >> A A A Dr. Axel Kohlmeyer A akohlmey_at_gmail.com A
> http://goo.gl/1wk0
> > >> A A A College of Science & Technology, Temple University,
> Philadelphia PA, USA
> > >> A A A International Centre for Theoretical Physics, Trieste.
> Italy.
> > >>
> > >> A A --
> > >> 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
> > >
> > > --
> > > 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.
>
> --
> 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. 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/