From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Tue Feb 04 2014 - 10:22:15 CST

Yay!

2014-02-04 Ming-Tsung Lee <mtlee_at_rci.rutgers.edu>:

> 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
>>
>
>

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607