Mailman 3 April 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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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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Trouble Importing yt
by sflarkin＠ucsc.edu 26 Apr '21

26 Apr '21

Hello All, I was having an issue with the yt.create_profile command, and I wanted to see if updating yt would help fix the issue. However, when I updated my anaconda yt installation to yt 3.6.1, I am now having this issue every time I try to load yt: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-1-3f99c158a398> in <module> ----> 1 import yt 2 import numpy as np 3 from yt import YTQuantity 4 5 import glob ~/anaconda3/lib/python3.7/site-packages/yt/__init__.py in <module> 61 display_ytarray 62 ---> 63 from yt.fields.api import \ 64 field_plugins, \ 65 DerivedField, \ ~/anaconda3/lib/python3.7/site-packages/yt/fields/api.py in <module> 17 field_plugins 18 ---> 19 from . import angular_momentum 20 from . import astro_fields 21 from . import cosmology_fields ~/anaconda3/lib/python3.7/site-packages/yt/fields/angular_momentum.py in <module> 24 register_field_plugin 25 ---> 26 from .vector_operations import \ 27 create_magnitude_field 28 ~/anaconda3/lib/python3.7/site-packages/yt/fields/vector_operations.py in <module> 30 handle_mks_cgs 31 ---> 32 from yt.geometry.geometry_handler import \ 33 is_curvilinear 34 ~/anaconda3/lib/python3.7/site-packages/yt/geometry/geometry_handler.py in <module> 27 from yt.utilities.io_handler import io_registry 28 from yt.utilities.logger import ytLogger as mylog ---> 29 from yt.utilities.parallel_tools.parallel_analysis_interface import \ 30 ParallelAnalysisInterface, parallel_root_only 31 from yt.utilities.exceptions import YTFieldNotFound ~/anaconda3/lib/python3.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py in <module> 28 29 from yt.config import ytcfg ---> 30 from yt.data_objects.image_array import ImageArray 31 import yt.utilities.logger 32 from yt.utilities.lib.quad_tree import \ ~/anaconda3/lib/python3.7/site-packages/yt/data_objects/image_array.py in <module> 16 from yt.config import \ 17 ytcfg ---> 18 from yt.visualization.image_writer import write_bitmap, write_image 19 from yt.units.yt_array import YTArray 20 ~/anaconda3/lib/python3.7/site-packages/yt/visualization/image_writer.py in <module> 24 from yt.units.yt_array import YTQuantity 25 from yt.utilities.exceptions import YTNotInsideNotebook ---> 26 from .color_maps import mcm 27 from . import _colormap_data as cmd 28 import yt.utilities.lib.image_utilities as au ~/anaconda3/lib/python3.7/site-packages/yt/visualization/color_maps.py in <module> 162 } 163 --> 164 add_colormap("cubehelix", _cubehelix_data) 165 166 # The turbo colormap, by Anton Mikhailov. ~/anaconda3/lib/python3.7/site-packages/yt/visualization/color_maps.py in add_colormap(name, cdict) 50 mcm.__dict__[name] = cdict 51 try: # API compatibility ---> 52 mcm.register_cmap(name, yt_colormaps[name]) 53 except AttributeError: 54 pass ~/anaconda3/lib/python3.7/site-packages/matplotlib/cm.py in register_cmap(name, cmap, override_builtin) 147 if not override_builtin and name in __builtin_cmaps: 148 msg = f"Trying to re-register the builtin cmap {name!r}." --> 149 raise ValueError(msg) 150 else: 151 msg = f"Trying to register the cmap {name!r} which already exists." ValueError: Trying to re-register the builtin cmap 'cubehelix'. I was wondering if anyone else had experienced a similar issue?

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(Another) Question About Yt Profiles
by sflarkin＠ucsc.edu 23 Apr '21

23 Apr '21

Hello All, I am doing some work using the yt.create_profile function, and it seems to be returning incorrect results, but that may be based just me misunderstanding something. I am currently working on collecting the dark matter profile within the virial radius of halos in an ART simulation, and have been using this create_profile function for a while. It was pointed out to me that two different profiles I created (one linearly spaced, and one logarithmacilly spaced seemed to disagree on the total mass in a given sphere. Upon looking into this I noticed that there appears to be a drastic falloff in mass for the inner most profiles which does not appear physical. Here is a script that shows the issue: import yt import numpy as np ds.quan(float(19.97536), 'Mpccm/h') center = [ds.quan(19.97536, 'Mpccm/h'), ds.quan(19.58991, 'Mpccm/h'), ds.quan(20.38296, 'Mpccm/h')] rvir = ds.quan(185.12684881603383, 'kpc') ds = yt.load('/Volumes/My Passport for Mac/VELAhalos_4_1_2021/GEN6/VELA07_snap/10MpcBox_csf512_a0.500.d') sp = ds.sphere(center, rvir) #space = np.logspace(-2,0,30) radius_bins = ds.arr(np.logspace(-2, 0, 30)*float(rvir), 'kpc') #print(radius_bins) #create the profile rp_darkmatter = yt.create_profile(sp, ('darkmatter', 'particle_radius'), [('darkmatter', 'particle_mass')], accumulation = True, units = {('darkmatter', 'particle_radius'): 'kpc', ('darkmatter', 'particle_mass'): 'Msun'}, weight_field=None, override_bins={('darkmatter', 'particle_radius'): radius_bins}) #now just find the mass within the smallest sphere to compare sp = ds.sphere(center, (1.85126849, 'kpc')) darkmatter_mass_rvir= sp.quantities.total_quantity([('darkmatter', 'particle_mass')]) Here is the outputs for the profile: print(rp_darkmatter.x_bins) print(rp_darkmatter[('darkmatter', 'particle_mass')]) [ 1.85126849 2.16987605 2.5433167 2.98102735 3.49406901 4.09540631 4.80023514 5.62636664 6.59467727 7.72963638 9.05992455 10.61915839 12.44673994 14.58885248 17.09962751 20.0425127 23.49187518 27.53488087 32.27369713 37.82807456 44.3383731 51.96910898 60.91311203 71.39639856 83.68388279 98.08607129 114.96690951 134.75297878 157.94427603 185.12684882] kpc [1.71640907e+09 4.08670014e+09 7.29731648e+09 1.15396909e+10 1.70891641e+10 2.43093919e+10 3.36631560e+10 4.56267933e+10 6.02872054e+10 7.78791509e+10 9.85060803e+10 1.22442170e+11 1.49759934e+11 1.80141955e+11 2.13532847e+11 2.51746816e+11 2.95421277e+11 3.46319791e+11 4.05501975e+11 4.73278346e+11 5.52642140e+11 6.41302652e+11 7.43654270e+11 8.45108184e+11 9.51028253e+11 1.06624695e+12 1.17616790e+12 1.29792900e+12 1.43690732e+12] Msun And here is the result for the two inner most spheres centered at the same center: 3597806296.1175537 Msun - 1.85126849 kpc 4420085989.534953 Msun - 2.16987605 kpc This is not the same mass as found by any of the inner spheres of the profile, and contains over twice as big as the inner most sphere. I have tried this for several radii, and it appears to always be off by a bit, but the difference gets smaller as the radii gets larger, as shown by a sphere for the total virial radius: 1440505125868.4753 Msun - 185.12684882 kpc Vs the total mass enclosed in the profile of 1.43690732e+12 (only about a 1% difference). I am wondering if there might be something wrong how I am using this, or if there is an issue with the profile maker. I had asked about profile before, and was told to use the rp_darkmatter.x, but rp_darkmatter.x_bins field for the radii. Has something been changed in this function? (Note, I have tried looking at the rp_darkmatter.x radii, but those also do not agree with a ds.sphere of the same radii) (PSS: This is using yt 3.5.1, as I tried to update to 3.6.1 and ran into an error importing yt)

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Help with Profile plot
by Edward Buie II 20 Apr '21

20 Apr '21

Hello, I hope whoever reading this is doing well. I am trying to make a 1D profile plot with a custom y label, however I am getting the error: AttributeError: 'ProfilePlot' object has no attribute 'set_ylabel' and I am confused. This is also the case when I try to set a xlabel. I am creating multiple profiles from 2 datasets by appending them to a list as is shown in the yt cookbook, I'm not sure if this would cause an error. Thank you -- Edward N. Buie II (he/him), *Ph.D. Candidate* Astrophysics School of Earth and Space Exploration (SESE) Arizona State University

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