Mailman 3 May 2021 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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Clump Finding for Gadget2 format
by 201s408s＠stu.kobe-u.ac.jp 21 Feb '22

21 Feb '22

Dear all, For my master's research, I installed yt and I want to load my research data converted to gadget2 format with yt. The function I want to use is the clump function, and I want to create a similar figure by performing the same processing as the Clump Finding below. https://yt-project.org/doc/cookbook/constructing_data_objects.html#cookbook… First of all, I tried to test with the gadget data placed in the data index, but neither the default nor the hdf5 format works. Is it possible to do Clump Finding in Gadget2 format?

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Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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refining rockstar-galaxies halo minimum mass
by C Bernhardt 14 Jun '21

14 Jun '21

Dear yt and rockstar users, I recently installed the newest version of rockstar-galaxies as I had been using a much older version. Although the output reports a particle mass of 1.31418e+05 Msun/h, I don't see any halos smaller than 1e+08 Msun/h. I was expecting to get the minimum masses an order of magnitude lower. I see in the config includes MIN_HALO_OUTPUT_SIZE = 25, set as a default. I tried to change this parameter to 10 and restart from the beginning, but I run rockstar within yt with RockstarHaloFinder ( yt.extensions.astro_analysis.halo_finding.rockstar.api), but my config file was overwritten by the defaults. Is this even the right approach? If so, how do I restart rockstar (more detailed than just rh.run(restart=True), please) with customized parameters within yt's RockstarHaloFinder? Thanks in advance, -- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik

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Registering external data as a Field of an existing dataset?
by Matthew Abruzzo 02 Jun '21

02 Jun '21

Hello, I wanted to ask if yt supports the registration of external data as a field of an existing dataset. In case it helps clarify my question, I just wanted to briefly elaborate on what I'm looking to do. I'm trying to characterize the turbulent velocities in some high resolution unigrid simulations. Because this involves convolution, I need to compute the turbulent velocity outside of the yt infrastructure (this seems beyond the scope of what a user-defined derived field can support). It would be convenient to be able to load the results back into yt to use the existing analysis machinery (e.g. for phase plots and slices). I have thought about using the "Generic Unigrid Data" frontend, but the simulation's size unfortunately makes that approach somewhat intractable. I'm pretty confident that the answer to my question is "no," but I wanted to be sure before I rolled my own solution. Thank you for your help. Best, Matthew Abruzzo

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Important NUMFocus Survey -- Please fill it out!
by Stephanie Tonnesen 31 May '21

31 May '21

Dear yt-ers, yt is participating in a research project being conducted by NumFOCUS <https://numfocus.org/>. The research is looking into understanding the diversity, inclusion and barriers to participation within NumFOCUS-sponsored projects and the wider open source community. The survey <https://numfocus.typeform.com/to/W6Bax8eq> will take 15-20 min to complete. We’d appreciate your contribution by June 8, 2021. The results of this survey will help NumFOCUS work closely with our projects to develop practices that will lead to project success around diversity, inclusion and sustainability. Click here to participate into the survey <https://numfocus.typeform.com/to/W6Bax8eq> Thank you in advance for your participation! Stephanie Tonnesen (for the yt steering committee) -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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Create a 3D fixed resolution buffer from 3D AMR data
by Tseng, Po-Hsun 23 May '21

23 May '21

Dear all, How to create a 3D fixed resolution buffer (FRB) from 3D AMR data? More specifically, if we would like to project 3D AMR data onto a 2D plane with fixed resolution, we can do something like below: proj = ds.proj(...) frb = proj.to_frb(...) plt.imshow(np.array(frb['density'])) However, if I understand correctly, the array `frb` stores 2D projected data instead of the original 3D data with fixed resolution, correct? How do I do that?. Thanks.

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Particle Bounds
by Zhang Meng 20 May '21

20 May '21

Hello All, I'm trying to find halos in mutiple snapshot files from DM-only cosmological simulation generated by Gadget-2, using FOF halo finder in yt. The box size of the simulation is 13.8Mpc/h and contain 1024^3 particles. Here is my code, data_ds = yt.load('./snapshot_016.0') hc = HaloCatalog(data_ds=data_ds, finder_method='fof',finder_kwargs={"dm_only":False,"ptype":"Halo"}) hc.create() and I met the error like this, yt.utilities.exceptions.YTDomainOverflow: Particle bounds (-386.63174, -385.38947, -525.52057) and (6900.443, 6900.271, 13799.999) exceed domain bounds [0. 0. 0.] code_length and [13800. 13800. 13800.] code_length. I have already updated yt and it's dependecy to the version 3.6.1, but I still have this problem. It seems like yt treat the particle velocity as the bound, I have no idea. What make me more confusing is there is no such error when I run above code for another small scale simualtion (886^3 particles and L_box=12Mpc/h), So, does anyone know what happend here or has ever met the same problem?

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Save The Dates!
by Stephanie Tonnesen 06 May '21

06 May '21

Hi yt-users, This is a quick note to ask you to save some time during the weeks of *June 7-11* and *August 2-6 *this year! We are going to try and push through PRs those weeks, with each week having its own theme! I hope that everyone can make both (meaning be active on slack and engaged in PRs)!! We will be sending out details with our vision for each week shortly. Mischief Managing week (we solemnly swear to be up to *only* good!) We will have a managing mischief week to focus on cleaning up the codebase. This is when we want dead code, code styling, and other PRs both submitted and merged. MM week will be on June 7-11 this year. PR Mentorship Week This is a week that we will help get older PRs and PRs from new contributors across the finish line. PRs from new contributors are always welcome; this week is specifically for extra focused time to boost the work of new contributors. This will include dedicated time from the development community on taking over PRs or mentoring newer contributors whose PRs have been waiting a while. PR Mentorship week will be held on August 2-6 this year. Can't wait to "see" you! -The yt steering committee -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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