Re: [hoomd-users] The gsd file becomes extremely large when logging quantities like forces and virials with Hoomd3.0

[Joshua Anderson]

Ren,

To reduce the size of the GSD files written by HOOMD-blue, you can store fewer frames in those files or store fewer per-particle data arrays in each frame.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

> On Jul 16, 2021, at 3:52 AM, Work Ren <rh....@gmail.com> wrote:
>
> Hi,
> When I am trying to log quantities like forces and virials etc with Hoomd3.0 into gsd file with 9000 particles, the size of the gsd file becomes extremely large, from about 100MB to about 3GB,
>
> The script I am using as the following:
>
> logger2 = hoomd.logging.Logger()
> logger2.add(lj, quantities=['energies', 'forces','torques','virials'])
> logger2.add(harmonic, quantities=['energies', 'forces','torques','virials'])
> logger2.add(angle, quantities=['energies', 'forces','torques','virials'])
> ...
> gsd_writer2 = hoomd.write.GSD(filename=log_gsd_file,
> dynamic=['momentum'],
> trigger=hoomd.trigger.Periodic(1000),
> mode='wb',
> filter=hoomd.filter.All(),
> log=logger2)
>
> Any suggestions to make the gsd file smaller?
>
> Thanks a lot
> Ren Hua
>
>
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[Work Ren]

Hi  Joshua,

Thank you very much for your reply, yes, I will try that.

Best Regards

Ren Hua

Joshua Anderson <joaa...@umich.edu> 于2021年7月20日周二 上午12:30写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/F0DAD5C9-2122-4C15-AABB-F2474F85CDD8%40umich.edu.