VMD-L Mailing List

From: Jan Janssen (janssen_at_mpie.de)
Date: Thu Nov 10 2016 - 01:29:50 CST

 Hello Axel,

Thanks for the quick reply. I tried the Linux Version and it worked better in terms that is was able to read in the file. It works fine for 2398638 Atoms, but even at this point I already get the error message: 

Info) Determining bond structure from distance search ...
ERROR) MolAtom 1460117: Exceeded maximum number of bonds (12).

When I then try to increase the size even further, to something like 6398642 atoms, the process crashes: 

Info) Determining bond structure from distance search ...
vmd_gridsearch_bonds (thread 4):  25.69 % complete
vmd_gridsearch_bonds (thread 0):  31.25 % complete
vmd_gridsearch_bonds (thread 8):  26.39 % complete
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Abort (core dumped)

So I was wondering if there is an option to disable the "Bond structure determination" especially for this kind of large samples? 

Regards

Jan

 From: Axel Kohlmeyer <akohlmey_at_gmail.com>
 To: Jan Janssen <janssen_at_mpie.de>
 Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
 Sent: 11/9/2016 7:21 PM
 Subject: Re: vmd-l: Limits of the VMD Visualisation

On Wed, Nov 9, 2016 at 11:59 AM, Jan Janssen <janssen_at_mpie.de> wrote:
> Hello,
>
> I guess this is not exactly the purpose of VMD, but we try to visualise an
> Atom Probe Dataset which we converted to *.xyz Format. The dataset consists
> of 6 million atoms and at least the Mac OS X Version of VMD crashed when
> trying to load the data, while loading a subset of the file worked fine.
> The question is whether we can compile VMD with special packages to support
> such large datasets or whether other file formats are more suitable for
> loading such large datasets. The file size is currently about 2GB.
 
current downloads of VMD for MacOSX are 32-bit (regardless of the CPU
and OS) and thus you are limited in your address space.
 
it should work on linux with a 64-bit binary.
 
axel.
 
>
> Regards
>
> Jan
>
>
>
>
> Crash:
> Info) Using plugin xyz for structure file /Users/jan/Desktop/pureAl_pos.xyz
> /Applications/VMD 1.9.3.app/Contents/MacOS/startup.command: line 7: 14731
> Segmentation fault: 11  "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> logout
> Saving session...
> ...copying shared history...
> ...saving history...truncating history files...
> ...completed.
>
>
> Head of the file:
> 60398640
> Atom probe data
> Al -8.14419269562 -44.8013191223 -14.9069433212
> Al -35.179271698 -3.4159450531 -8.59115982056
> Al -15.6410989761 -25.2453269958 -5.95746135712
> Al 1.84774339199 -44.2051582336 -13.9800004959
> Al 6.15377855301 -44.0587081909 -14.1510372162
> Al 17.3810424805 -50.0091285706 -21.0890655518
> Al -22.3692836761 -40.944026947 -15.7445049286
> Al -0.755965948105 -44.747303009 -14.3411016464
>
>
>
>

 
 
 
--
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.

 

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