Re: [yt-dev] yt Particle Plots & openPMD Frontend

Hey, The issue you're having is because you're constructing known_other_fields dynamically. All the other frontends define it statically, so it's filled out by the time it's needed in the `setup_fluid_aliases` function defined in in yt/fields/field_info_container.py. The fix is to change the order of operations - setup known_other_fields and known_particle_fields before calling the __init__ method on the superclass of OpenPMDFieldInfo. You're also incorrectly setting the units of the field to a Unit object --- the unit entry in the known_other_fields tuple should be a string. The following diff allows me to set the units properly for your frontend: http://paste.yt-project.org/show/6606/ Out of curiosity - why build the known_other_fields and known_particle_fields tuples dynamically? The reason they're static for all the other frotends is to make it easy to reason about which fields are associated with a given frontend and so that the fields known by a given frontend are independent of any particular dataset you might be looking at. By the way, it also looks like the 'all' particle union is working correctly - are you still having issues with that? -Nathan On Fri, Jun 10, 2016 at 8:24 AM, Fabian Koller wrote:

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 mailto:a.huebl@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 mailto:a.huebl@hzdr.de > mailto:a.huebl@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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