VMD-L Mailing List

From: Ming-Tsung Lee (mtlee_at_rci.rutgers.edu)
Date: Tue Feb 04 2014 - 10:08:26 CST

Olaf,

Thank you very much for the efforts. I confirm that by loading your dll
file, VMD can now load the VTF files generated by DL_MESO on my Windows
system.

Best Regards,
MT

Ming-Tsung Lee
Department of Chemical & Biochemical Engineering
Rutgers, The State University of New Jersey
98 Brett Road
Piscataway, NJ 08854
tel: 848-445-6953

On Tue, Feb 4, 2014 at 9:32 AM, Olaf Lenz <olenz_at_icp.uni-stuttgart.de>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.
>
> At
> 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 use
>
> 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,
>> > Most likely this is an issue with uninitialized data, a buffer
>> overrun,
>> > or something similar. Have you done tests with the failing input using
>> > valgrind on Linux? If not, I'd try that first. 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. 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,
>> > John
>> >
>> > On Mon, Feb 03, 2014 at 07:09:13PM +0100, Olaf Lenz wrote:
>> >> Hi!
>> >>
>> >> The trouble is that I do not have access to a Windows development
>> system.
>> >> With your message, I can have a look at the code again, but I am
>> unable to
>> >> compile or debug under Windows.
>> >>
>> >> Olaf
>> >>
>> >> Dr. rer. nat. Olaf Lenz
>> >> Institut fA 1/4r Computerphysik, Allmandring 3, D-70569 Stuttgart
>> >> Phone: +49.711.685.63607
>> >>
>> >> Am 03.02.2014 18:51 schrieb "Ming-Tsung Lee" <mtlee_at_rci.rutgers.edu
>> >:
>> >>
>> >> Hi Olaf,
>> >> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22262.html
>> >> I think that I probably find the bug. In the VTF file generated by
>> >> DL_MESO (attached, not sure the situation of ESPresSo). In the
>> first
>> >> frame of the trajectory, box dimensions are defined as follows
>> >> timestep indexed
>> >> pbc A 15.000000 15.000000 15.000000
>> >> A A A A 0 10.867398 12.150888 14.039090
>> >> A A A A 1 A 9.467130 10.474655 12.615115
>> >> A A A A 2 A ...
>> >> I have checked the default syntax of VTF. The box angles should be
>> >> optional.
>> >> https://github.com/olenz/vtfplugin/wiki/VTF-format
>> >> I have played that around. It looks like that VMD is frozen while
>> >> loading the line pbc/unitcell, as long as there are no "90 90 90"
>> >> assigned. Nevertheless, the same VTF works perfectly well with
>> the Linux
>> >> version VMD. Would you please check your plugins for both
>> platforms?
>> >> Probably something is messed up in the Windows version. Thank you.
>> >> For those who are using DL_MESO and want a quick solution for
>> this,
>> >> simply modify the trajectory output by putting a "90 90 90" after
>> your
>> >> box dimensions. It will work.
>> >> Best,
>> >> MT
>> >> P.S. I am using Windows 7 x64 enterprise, VMD 1.9.1. Trajectory is
>> >> generated from DL_MESO/DEMO/Polyelectrolyte/HISTORY, using
>> >> /DL_MESO/DPD/utility/trajectselected.f90A
>> >> Ming-Tsung Lee
>> >> Department of Chemical & Biochemical Engineering
>> >> Rutgers, The State University of New Jersey
>> >> 98 Brett Road
>> >> Piscataway, NJ 08854
>> >> 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/ 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.
>>
>
>
>
> --
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
> Phone: +49-711-685-63607
>