VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 09 2016 - 12:21:13 CST

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
>
>
>
>
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-- 
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.