VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 10 2016 - 01:45:01 CST

Hi,
  Try running this command on the text interface in VMD:
mol new yourfile.xyz autobonds off

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 10, 2016 at 08:29:50AM +0100, Jan Janssen wrote:
> 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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