VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 04 2014 - 10:29:13 CST

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.