VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 03 2014 - 13:21:47 CST

On Mon, Feb 3, 2014 at 1:09 PM, Olaf Lenz <olenz_at_icp.uni-stuttgart.de> 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.

i have successfully compiled plugins for windows using the mingw64
toolchain on (fedora) linux and run standalone test binaries through
wine also on linux. it should also be possible to run gdb, but i - so
far - only tried that with a virtual machine.
please also note that VMD 1.9.1 doesn't have the latest revision of
the plugin, since there hasn't been a VMD release for quite a while.

if it works well on linux, even if the files are generated on windows,
then i would suggest to first try compiling a version for windows that
opens files in binary mode ("rb" instead of "r"), because the
automatic CR-LF translation of windows can easily wreak havoc when
parsing files.

axel.

>
> Olaf
>
> Dr. rer. nat. Olaf Lenz
> Institut für 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 15.000000 15.000000 15.000000
>> 0 10.867398 12.150888 14.039090
>> 1 9.467130 10.474655 12.615115
>> 2 ...
>>
>> 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.f90
>>
>> 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 

-- 
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.