[yt-dev] yt Particle Plots & openPMD Frontend
Fabian Koller
f.koller at hzdr.de
Fri Jun 10 06:24:46 PDT 2016
Cheers Nathan,
thank you for the patch. I pulled the code (#2213) into my local copy
and gave it as in-depth a test as I could. It works, except for one detail.
I am unsure whether the problem arises from the frontend or through the
unit system, but what I am currently facing is: fields from
known_other_fields do not have units (ergo are dimensionless) in
datasets, no matter what the unit in known_other_fields.
I've attached a script which tries to show the problem by using one of
the example files Axel linked to in his last mail.
--Fabian
On 03/06/16 23:05, Nathan Goldbaum wrote:
> I've opened a pull request to fix the issue you discovered with
> magnetic units:
>
> https://bitbucket.org/yt_analysis/yt/pull-requests/2213
>
> I'd appreciate it if one of you could give it a test. Let me know if
> you have questions about how to pull a pull request in locally with
> mercurial.
>
> I haven't had a time to look at the issue you were having with the
> 'all' particle union, but I have it on my list to look at it.
>
> On Fri, May 27, 2016 at 2:37 AM, Huebl, Axel <a.huebl at hzdr.de
> <mailto:a.huebl at hzdr.de>> wrote:
>
> Dear Nathan and John,
>
> thank you for the quick answers.
>
> Yes, the resources to reproduce the questions are:
>
> Repo:
> https://bitbucket.org/C0nsultant/openpmd/src?at=yt
>
> Example Files:
> PIConGPU > 2D3V > one of the .h5 files
> https://owncloud.hzdr.de/index.php/s/ouisGZe5M0wCVzj
> password: openPMD
>
> Example script (attached, like last mail).
>
>
> Axel
>
> On 24.05.2016 18 <tel:24.05.2016%2018>:37, Nathan Goldbaum wrote:
> >
> >
> > On Tue, May 24, 2016 at 11:30 AM, Huebl, Axel <a.huebl at hzdr.de
> <mailto:a.huebl at hzdr.de>
> > <mailto:a.huebl at hzdr.de <mailto:a.huebl at hzdr.de>>> wrote:
> >
> > Hi yt-devs,
> >
> > I am forwarding this conversation to the public list to keep
> it open for
> > others to join in and to build up a record that might help
> others.
> >
> > Our new student Fabian updated our frontend and implemented
> particle
> > readers. Unfortunately some details of the particle "fields"
> still cause
> > some bumps that we can not get our head around.
> >
> > We are now able to read fields and particles, even
> chunk-wise, and can
> > work with the data we read in python scripts via the
> all_data() method.
> >
> > Nevertheless, using the particle scatter plots such as
> yt.ParticlePlot
> > seems not to work. We have some problems with unions / the
> "all" group
> > and the fact that we have several particle species (e.g., "hot
> > electrons", "cold electrons", "helium ions", "nitrogen
> ions", etc.)
> >
> >
> > The 'all' particle union should get set up automatically, but maybe
> > something is going wrong with that machinery.
> >
> > Can you create a test script that illustrates this issue using a
> > publicly available OpenPMD dataset?
> >
> >
> >
> > Also since the last rebase: did someone recently change the
> unit system
> > in yt? T for "Tesla" seems not to be understood any more. Is
> there a
> > changelog somewhere available? Do we have to describe our
> data in
> > cgs / mks?
> >
> >
> > I just double-checked, and Tesla should be working:
> >
> > In [1]: from yt import YTQuantity
> >
> > In [2]: YTQuantity(1, 'T')
> > Out[2]: 1.0 T
> >
> > In [3]: YTQuantity(1, 'T').to_equivalent('G', 'CGS')
> > Out[3]: 10000.0 G
> >
> > Can you explain a little bit more what issue you're having? A test
> > script that illustrates the issue would also help.
> >
> >
> > Would someone be interested for a quick heads up via e.g.,
> skype /
> > web-rtc so we can ask specific questions?
> >
> > Fabian is around on Tuesdays and Fridays, something like
> early CA time,
> > and late GER time usually works great (e.g., 9pm-PDT /
> 6pm-CEST).
> >
> > Our current branch HEAD can be found here
> (->yt->frontends->openPMD):
> > https://bitbucket.org/C0nsultant/openpmd/src?at=yt
> >
> > And an example script is attached.
> >
> >
> > Thanks a lot!
> > Axel
> >
> >
>
> --
>
> Axel Huebl
> Phone +49 351 260 3582 <tel:%2B49%20351%20260%203582>
> https://www.hzdr.de/crp
> Computational Radiation Physics
> Laser Particle Acceleration Division
> Helmholtz-Zentrum Dresden - Rossendorf e.V.
>
> Bautzner Landstrasse 400, 01328 Dresden
> POB 510119, D-01314 Dresden
> Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
> Prof. Dr.Dr.h.c. P. Joehnk
> VR 1693 beim Amtsgericht Dresden
>
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