Mailman 3 July 2020 - 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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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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comoving scale annotation?
by Salome Mtchedlidze 05 Dec '20

05 Dec '20

Hello again, I am using yt slices and projections with scale annotation. I have my plots in comoving units ("Mpccm/h") but whenever I want to use the same units for annotation: slc.annotate_scale(corner='lower_right', coeff=10, units='Mpccm/h'), yt does not recognize these units. Am I missing something or only the physical scale annotation is possible ? Thanks, Salome

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Adding divergence field
by Michael Jennings 08 Aug '20

08 Aug '20

Hi all, I am attempting to add a divergence field and am running into the issue apparent in the plot below: The grid artifacts appear to be the meshblocks for mpi parallelization when running the simulation. This doesn’t occur for any other field. I am working with an Athena++ athdf dataset and using yt version 3.7.dev0. Here is the script I used to add the desired field: import yt from yt.fields.derived_field import ValidateSpatial import yt.units as u kappa0 = 9.68e4 ds = yt.load('../pleiades/grf/grf_pr_2_3_nm5_3/TI.uov.00200.athdf',\ units_override=units_override,unit_system="cgs") grad_fields = ds.add_gradient_fields(("gas","temperature")) def _therm_cond(field,data): kappa = kappa0*u.erg/(u.cm*u.K*u.s) sl_left = slice(None, -2, None) sl_right = slice(2, None, None) div_fac = 2.0 ds = div_fac * data['dx'].flat[0] f = data["temperature_gradient_x"][sl_right,1:-1,1:-1]/ds f -= data["temperature_gradient_x"][sl_left ,1:-1,1:-1]/ds if data.ds.dimensionality > 1: ds = div_fac * data['dy'].flat[0] f += data["temperature_gradient_y"][1:-1,sl_right,1:-1]/ds f -= data["temperature_gradient_y"][1:-1,sl_left ,1:-1]/ds if data.ds.dimensionality > 2: ds = div_fac * data['dz'].flat[0] f += data["temperature_gradient_z"][1:-1,1:-1,sl_right]/ds f -= data["temperature_gradient_z"][1:-1,1:-1,sl_left ]/ds new_field = np.zeros(data["temperature_gradient_x"].shape, dtype='float64') new_field = data.ds.arr(new_field,'K/cm**2') new_field[1:-1,1:-1,1:-1] = f return kappa*new_field/data['density'] ds.add_field(('gas','therm_cond'), function=_therm_cond, units="erg/(g*s)", sampling_type="cell", take_log=False, display_name=r'$\nabla \cdot (\kappa\nabla T)/\rho$', force_override=True, validators = [ValidateSpatial(1, ['temperature_gradient_x','temperature_gradient_y','temperature_gradient_z'])]) Has anyone come across this issue before? Is this a known bug or am I just implementing the divergence field incorrectly? Any help is greatly appreciated. Thanks, Michael

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FLASH Nearest Neighbor - yt 3.6.0
by clp3ef＠virginia.edu 06 Aug '20

06 Aug '20

Hi! I'm working with a FLASH dataset and am trying to use the add_nearest_neighbor_field() function as briefly described here https://yt-project.org/doc/analyzing/fields.html#computing-the-nth-nearest-…. However, when I run the short script (with the input data replaced with my own FLASH dataset), I get the errors yt.fields.field_exceptions.NeedsGridType: (0, None) and NotImplementedError. Is this function not available for FLASH datasets, and is there a workaround? My final goal is to create a smoothed particle field, so if there is a better way than using the nearest_neighbor_distance_64 field in place of a smoothing_length field, please let me know! Input data: plt file - http://use.yt/upload/a94cdffd part file - http://use.yt/upload/dec62ce5 Test Script: http://paste.yt-project.org/show/259/ Camryn

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Ellipticity/axes of the 3D
by Robin Eappen 06 Aug '20

06 Aug '20

Hi, Just wondering if it is possible to find the ellipticity of the model. I assume one should first start with all the (x,y,z) coordinates and fit them to an ellipsoid. Is it already implemented in yt? Thank you Robin

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_png error
by Steiner, Andrew (Andrew W. Steiner) 29 Jul '20

29 Jul '20

Hello all, After installing yt 3.6.0 and matplotlib 3.3.0 on 10.15.6 I'm getting the error below after running 'import yt' regarding matplotlib._png. Any ideas? Thank you, Andrew import yt File "/usr/local/lib/python3.8/site-packages/yt/__init__.py", line 63, in <module> from yt.fields.api import \ File "/usr/local/lib/python3.8/site-packages/yt/fields/api.py", line 19, in <module> from . import angular_momentum File "/usr/local/lib/python3.8/site-packages/yt/fields/angular_momentum.py", line 26, in <module> from .vector_operations import \ File "/usr/local/lib/python3.8/site-packages/yt/fields/vector_operations.py", line 32, in <module> from yt.geometry.geometry_handler import \ File "/usr/local/lib/python3.8/site-packages/yt/geometry/geometry_handler.py", line 29, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/usr/local/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 30, in <module> from yt.data_objects.image_array import ImageArray File "/usr/local/lib/python3.8/site-packages/yt/data_objects/image_array.py", line 18, in <module> from yt.visualization.image_writer import write_bitmap, write_image File "/usr/local/lib/python3.8/site-packages/yt/visualization/image_writer.py", line 29, in <module> import yt.utilities.png_writer as pw File "/usr/local/lib/python3.8/site-packages/yt/utilities/png_writer.py", line 13, in <module> import matplotlib._png as _png

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A virtual yt showcase meeting?
by Stephanie Tonnesen 23 Jul '20

23 Jul '20

Hi yt-users! I am often surprised by all the capabilities of yt that can help me with my research. I think a workshop in which participants shared how they use yt for their research could be really informative and fun. Tentative name: "*R*esearc*H* utilizing *yt* *H*ighlights *M*eeting: *RHytHM*, no blues". I think it would be a virtual meeting this winter. Please let me know if anyone else thinks this idea is interesting, and if so I will try to make it happen! Thanks, Stephanie https://www.doodle.com/poll/7my9e6s7x9h7i6c5 <https://slack-redir.net/link?url=https%3A%2F%2Fwww.doodle.com%2Fpoll%2F7my9…> (edited) PS Sorry if you also read this on the #random channel! -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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Projection Plot: Finer Resolution than 800x800 Fixed Resolution Buffer
by euan.newlands＠gmail.com 21 Jul '20

21 Jul '20

Hello! I am having trouble improving the resolution of my ProjectionPlot() of a density field. I have studied the documentation (attached below) and can't see a solution to my problem. I am trying to obtain a projection plot of an isolated galaxy from a 25Mpc box, using a data sphere as the data source for the projection. The default plot settings makes "a fixed resolution buffer of (('gas', 'density')) 800 by 800". When I use .set_buff_size(1000) for example, the resolution does not change - I'm assuming because the plot has already been plotted with buff size 800x800 and thus this is the 'max' buff size and cannot be reduced. However when I use a lower buff size, i.e. .set_buff_size(400), the resolution worsens and I am left with a horrifically pixelated projection plot. Can you help me identify a method to decrease the bin size of the density bins so I have a more detailed density projection plot? Thanks for your time. https://yt-project.org/doc/reference/api/yt.visualization.plot_window.html?…

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possible difference between sphere and cut_region selections
by Stephanie Tonnesen 21 Jul '20

21 Jul '20

Hi yt-users! I have a list of positions that I call xwclump, ywclump, and zwclump. I have been selecting regions in a loop using ds.sphere and the center: data_source = ds.sphere([xwclump[j]/(300.*3.086e21),ywclump[j]/(300.*3.086e21),zwclump[j]/(300.*3.086e21)],(1000,'pc')) (the divisor is to put the center into code units). This works fine. But, when I try to use cut_region: data_source = ad.cut_region(["(obj['temperature'] > 1.0e6) & (obj['z'] < (zwclump[j]/(300.*3.086e21)))"]) I get an error: NameError: name 'zwclump' is not defined Is this something anyone else has dealt with? If it doesn't ring any bells I will try and break IsolatedGalaxy and send the code snippet... Thanks, Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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yt-users July 2020