Mailman 3 March 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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Wrong particle IDs in the sphere
by h.fathie＠gmail.com 31 Mar '21

31 Mar '21

Dear all, I have read a Gadget snapshot as follows: ds = yt.load('../GadgetDiskGalaxy/snapshot_200.hdf5') partID = ad[('PartType0', 'ParticleIDs')] I then defined a sphere around a Type0 particle using the following lines of code: j = 9000 sp = ds.sphere([px[j],py[j],pz[j]],(20.0,'kpc')) When I issue the following command: print(sp["particle_index"]) I get: [ 841624. 890649. 841457. 890473. 865599. 865772. 6258099. 5752659. 5752660. 5777940. 6229883. 5803543.] dimensionless This shows that there are 12 particles inside the sphere. I checked and found that the following IDs exist in the 'partID' array: 841624. 890649. 841457. 890473. 865599. 865772. but these IDs (see below) do NOT exist in the 'partID' array: 6258099. 5752659. 5752660. 5777940. 6229883. 5803543 So the IDs of these 6 particles inside the sphere do not exist in the 'partID' array. How is this possible since 'partID' (as defined above) must contain the IDs of all Type0 particles ? I would be grateful if someone could help me with this issue. Best regards, Hassan

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Reading a large RAMSES snapshot
by Ankit Singh 24 Mar '21

24 Mar '21

Hi, I am trying to read a RAMSES snapshot which has a size of a few TB. Please let me know what are methods I can use to read this using yt. I have good computation available but I can see from here: ( https://yt-project.org/doc/analyzing/parallel_computation.html) that yt can't perform the reading operation in parallel. I tried using bbox argument to get a smaller region but that didn't help. I would really appreciate any help in this regard. Thanks, Ankit Singh

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Post processing dust evolution in Simulations
by h.fathie＠gmail.com 13 Mar '21

13 Mar '21

Dear all, I have a simulation of an isolated galaxy with dark matter, bulge stars, disk stars and gas particles. I would like to probe how dust evolves over time by post processing this simulation. I am new in this subject and I would be very grateful if some one could introduce some references or post-processing libraries, or ... that could be used to trace dust evolution in simulations. Many thanks in advance. Best regards, Hassan

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question about spheres
by Stephanie Tonnesen 09 Mar '21

09 Mar '21

Hi yt-users, I have a question about spheres, because I am having a problem that I don't really know how to solve. Basically, I have clusters of stars, and I want to know how many stars are within 6 pc of each star. So, what I have done is taken a sphere at each star position with a radius of 6 pc, and then performed sp.quantities.total_quantity(["particle_mass"]) Now I wanted to double-check this number by brute-force, so I calculated the distance between all the particles and then summed the masses of all the particles that were less than 6 pc. I am not getting the same values--they are close, but not the same (they seem to mostly scatter up or down by a factor of 2). So...to the question!! Because I am measuring particles in a grid code (Enzo) is there any sort of shifting to the grid position instead of using the particle positions here? Because stars are pretty packed I could imagine that this could cause the differences I am seeing. I am not sure that the problem is not something silly I am doing, but wanted to check this possibility as well. Thanks! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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refining rockstar-galaxies halo minimum mass
by C Bernhardt 08 Mar '21

08 Mar '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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triage meetings -- early 2021!
by Madicken Munk 03 Mar '21

03 Mar '21

Hi yt-users! It's been a while since we've had scheduled triage meetings during the week. We use triage meetings to do development and maintenance work on the project. If you'd like to help contribute to making yt *better* and maybe even more useful for you, consider attending! All skill levels in development are welcome and encouraged to attend. If you're a bit shy, don't worry, you can also attend and just listen! I've created two polls. The first is morning in central US timezone to hopefully catch times where project members located in Europe can join, and the second is for afternoon/early evening in the central US timezone so project members on the west coast and asia can hopefully join. Vote in whatever poll applies to you (or both if you find all times work). We will choose times to accommodate the most people, and I personally would love to see all of you attend!!! I've put times for next week, but know that these polls are your *general availability *weekly for the next few months. Morning Poll: http://whenisgood.net/tmdfp2i Afternoon Poll: http://whenisgood.net/i2c8n3b - Madicken

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