Mailman 3 June 2021 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 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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Problems with running Rockstar from Yt
by Nick Gnedin 13 Jul '21

13 Jul '21

It appears that Yt does not run Rockstar correctly. Here are 2 issues we discovered so far: 1. DM particle mass and hence halo masses are incorrect in a simulation with baryons. Here are lines from one of out_*.list for a simulation with 1024^3 particles in a 40 cMpc/h box: #Om = 0.303600; Ol = 0.696400; h = 0.681400 #Particle mass: 4.22991e+06 Msun/h The particle mass should be 2.77536623e11*0.3036/0.6814*40**3/1024**3 = 7370552 Msun Instead, the reported value is 4.22991e+06 Msun/h = 6207675 Msun, which is exactly 2.77536623e11*0.2557/0.6814*40**3/1024**3 and 0.2557 = Omega_{DM}, not Omega_M. The same incorrect value is reported independently of what I set for the dm_only argument to RockstarHaloFinder. In a DMO simulation with identical initial conditions the particle mass is reported correctly: #Particle mass: 5.02229e+06 Msun/h This is for the snapshot read by the artio frontend. 2. I tried to circumvent the previous bug by setting particle_mass=5.02229e+06 in the call to RockstarHaloFinder, but that dies with the following error: p['particle_mass'].convert_to_units("Msun / h") P002 yt : [ERROR ] 2021-06-01 19:17:19,937 AttributeError: 'float' object has no attribute 'convert_to_units' It appears that the argument of particle_mass keyword must be some class rather than a number as listed in the documentation. 3. When running on a simulation with a non-zero DC mode Yt sets the box size incorrectly: > fgrep '#Box size' out_* out_0.list:#Box size: 40.216236 Mpc/h out_1.list:#Box size: 40.216236 Mpc/h ... out_14.list:#Box size: 40.216236 Mpc/h It appears that Yt uses the value Lbox*abox/auni for the first snapshot, and never recomputes it for the following snapshots. That corrupts halo positions, and, what is even worse, applies periodic wrapping incorrectly, so halos near the box boundaries are messed up. Nick Gnedin -- This email has been checked for viruses by AVG. https://www.avg.com

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Question about linking yt with rockstar
by Jessica López 21 Jun '21

21 Jun '21

Hello, I've installed yt and yt_astro_analysis since the source as well as rockstar-galaxies (according to the instructions in the web page) in order to use the halo finder. Then, in my script I have from yt.extensions.astro_analysis.halo_analysis import HaloCatalog import yt data=yt.load("/home/user/Programas/enzo-dev/run/CosmologySimulation/amr_cosmology/DD0010/DD0010") halo=HaloCatalog(data_ds=data,finder_method='rockstar') halo.create() However it appears the error message ---------------------------------------------------------------------------TypeError Traceback (most recent call last)<ipython-input-5-3ebc8a5b69aa> in <module> 5 es = yt.load("/home/jessica/Programas/enzo-dev/run/CosmologySimulation/amr_cosmology/DD0010/DD0010", "Enzo") 6 hc = HaloCatalog(data_ds=es, finder_method='rockstar', finder_kwargs={"num_readers": 2, "num_writers": 4})----> 7 hc.create() ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py in create(self, save_halos, save_output, njobs, dynamic) 331 """ 332 --> 333 self._run(save_halos, save_output, 334 njobs=njobs, dynamic=dynamic) 335 ~/.local/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py in barrierize(*args, **kwargs) 299 def barrierize(*args, **kwargs): 300 if not parallel_capable:--> 301 return func(*args, **kwargs) 302 mylog.debug("Entering barrier before %s", func.__name__) 303 comm = _get_comm(args) ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py in _run(self, save_halos, save_catalog, njobs, dynamic) 222 # Find halos. 223 if self.halos_ds is None:--> 224 self.finder_method(self) 225 return 226 ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py in __call__(self, hc) 37 38 def __call__(self, hc):---> 39 return self.function(hc, *self.args, **self.kwargs) 40 41 def _hop_method(hc, **finder_kwargs): ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py in _rockstar_method(hc, **finder_kwargs) 85 86 ds = hc.data_ds---> 87 rh = RockstarHaloFinder(ds, **finder_kwargs) 88 rh.run() 89 ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py in __init__(self, ts, num_readers, num_writers, outbase, particle_type, star_types, force_res, initial_metric_scaling, non_dm_metric_scaling, suppress_galaxies, total_particles, dm_only, particle_mass, min_halo_size) 212 # Decide how we're working. 213 if ytcfg.get("yt", "inline"):--> 214 self.runner = InlineRunner() 215 else: 216 self.runner = StandardRunner(num_readers, num_writers) ~/Programas/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py in __init__(self) 42 def __init__(self): 43 # If this is being run inline, num_readers == comm.size, always.---> 44 psize = ytcfg.get("yt", "internals", "global_parallel_size") 45 self.num_readers = psize 46 # No choice for you, everyone's a writer too! ~/.local/lib/python3.8/site-packages/yt/config.py in get(self, section, option, *args, **kwargs) 135 136 def get(self, section, option, *args, **kwargs):--> 137 val = super(YTConfigParser, self).get(section, option, *args, **kwargs) 138 return os.path.expanduser(os.path.expandvars(val)) 139 TypeError: get() takes 3 positional arguments but 4 were given ------------------------------------------------------------------------- How can I fix this? Thank you in advance

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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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Question about Converting Between Various Gas Fields
by sflarkin＠ucsc.edu 05 Jun '21

05 Jun '21

Hello All! I am having some trouble understanding the interplay between a few gas fields, namely ('gas', 'density'), ('gas', 'cell_mass'), and ('gas', 'cell_volume'). Looking at the O/H ratios at various radii for some galaxies has lead me to some confusion in how to properly convert between these . I am using a script like this to construct a sphere of a given radius (here 10% of the virial radius) and find the mass of the gas within it: ###BEGIN SCRIPT import yt ds = yt.load('/Volumes/My Passport for Mac/VELAhalos_4_1_2021/GEN6/VELA07_snap/10MpcBox_csf512_a0.500.d') x = ds.quan(19.97536, 'Mpccm/h') y = ds.quan(19.58991, 'Mpccm/h') z = ds.quan(20.38296, 'Mpccm/h') center = [x,y,z] radius = yt.YTQuantity(185.12684881603383 , 'kpc') sp_10percent = ds.sphere(center, radius * 0.1) gas_density, gas_volume, gas_mass = sp_10percent.quantities.total_quantity([('gas', 'density'), ('gas', 'cell_volume'), ('gas', 'cell_mass')]) ##END SCRIPT This script returns these values: gas_density = 11770623025851.596 Msun/kpc**3 gas_volume = 26575.843162683213 kpc**3 gas_mass = 15826330839.340445 Msun Now, from what I understood, the gas_mass field is derived from the gas_density * gas_volume (from this page https://yt-project.org/doc/reference/field_list.html). However, doing that calculation returns a value around 10^16 Msun, not anywhere close to the 10^9 value returned by the cell_mass field. I am wondering the proper way to manually convert from the gas_density to the cell_mass field, and I am clearly missing something in my understanding. I would like to be able to do this outside of yt for convenience as the 'art', 'Metal_Density_SNII' field only returns a density, and not a mass, which I would like to study, so where do I look to find the proper conversion? Or is my understanding of one of the above fields lacking in some way? Thank you for your time and convience!

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IMPORTANT: DELAY of Managing Mischief Week!
by Stephanie Tonnesen 02 Jun '21

02 Jun '21

Dear all, I apologize, but after my email yesterday the steering committee discussed and decided that right now we are *this close* to the yt-4.0 release, and rather than give a Managing Mischief week half our attention and enthusiasm we should postpone. Therefore, *Managing Mischief week is NOT happening next week*. We really want this virtual yt MM week to be a success, and hopefully give us something to work off of for future yt-hack weeks, so it *will* happen this summer, just not in June. Please hang on to your excitement about this, and we will let you know well in advance of the rescheduled dates. And...get excited for the yt-4.0 release, coming soon! Thank you all for your understanding and patience, Stephanie (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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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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Managing Mischief NEXT WEEK!
by Stephanie Tonnesen 02 Jun '21

02 Jun '21

Dear yt-ers! Next week is our first attempt at a completely virtual yt hack week, so we hope you can join in to make it a success! *The goal of this week is "Managing Mischief"--This is when we want dead code, code styling, and other PRs both submitted and merged. We can take a look at YTEPs that have been waiting for our attention as well!* This is a pretty open-ended week, with the goal being to push through these refactoring-type PRs. If you want to be involved, but aren't sure where to start, some of the steering committee will be "on-call" throughout the week on slack so you can ask them what people are working on, or who to ask to take a look at the PR you are working on. We are letting this be self-driven, so if you and someone else are hashing out something and want to zoom, go for it! If slack and github messaging are getting the job done, stick with that! If you want a third mind on a call/github discussion to help out, ask! *Let's try using the #development channel for most of this discussion on slack. *Post here the PRs you are working on so others can join in! Post here your questions about code style! Post here your frustration that you can't pass that last fido test! *So you know you are not alone, here is when we will definitely be online thinking yt thoughts. *These are NOT comprehensive (you may get a response very quickly outside of these times!), but you can expect a quick response during these days and times: Monday (June 7): 12 pm - 2pm UTC: Matt Turk and Britton Smith 6 pm - 8 pm UTC: John ZuHone and Cameron Hummels Tuesday (June 8): 1 pm - 3 pm UTC: Matt Turk and Britton Smith 6 pm - 8 pm UTC: Matt Turk and John ZuHone Wednesday (June 9): 2 pm - 4 pm UTC: Britton Smith and John ZuHone Thursday (June 10): 3 pm - 4 pm UTC: Matt Turk and Britton Smith 4 pm - 5pm UTC: Matt Turk and John ZuHone Friday (June 11): 2 pm - 3 pm UTC: Matt Turk and John ZuHone 7 pm - 8 pm UTC: Matt Turk and John ZuHone Can't wait to hack away next week! --Your friendly neighborhood yt steering committee -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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