Mailman 3 August 2020 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 15, 2022

Aug. 15, 2022

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 Dec. 11, 2021

Dec. 11, 2021

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 Dec. 5, 2020

Dec. 5, 2020

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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spatial positions in FLASH code
by Thibault Goudal Aug. 26, 2020

Aug. 26, 2020

Hi! Working on the FLASH code (dynamic mesh refinement), I am looking for how could I get from the HDF5 Outputs the spatial positions (in physical units). Idealy, if I run a 2D simulation, I would like to obtain x and y arrays at a given time. It is not necessarally a YT issue but it is obvious that some modules could help a lot. Tell me if you have any idea! Thanks -- Thibault Goudal PhD Student CEA CELIA CNRS UMR5107 laboratory +33664160842 thibault.goudal(a)u-bordeaux.fr

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annotate_quiver
by Prateek Gupta Aug. 10, 2020

Aug. 10, 2020

Dear all, I am trying to annotate quiver over the projection plot of density field using the following code line: * p.annotate_quiver("velocity_x", "velocity_y", factor = 35, normalize = True, plot_args = {"color":'Red'})* but it shows an *error*: File "/home/user1/yt/yt/visualization/plot_window.py", line 997, in run_callbacks callback = CallbackMaker(*args[1:], **kwargs) *TypeError: __init__() got an unexpected keyword argument 'plot_args'* Without *'plot_args'* keyword argument annotation works fine but I need to adjust the color and the width of the vectors. I am using yt Version = 3.5.dev0. It may be a silly question: while annotating vectors (velocity_x and velocity_y, say) over the projection plot, is the annotation done after the weighted line integration of velocity_x and velocity_y over the width of the projection? and for this also the weight field is the same as we specified in the field projection method! If so, Is there any way to change the weight field for the annotation? Many thanks and regards, -Prateek

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Adding divergence field
by Michael Jennings Aug. 7, 2020

Aug. 7, 2020

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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Using 'density' method for smooth() function
by clp3ef＠virginia.edu Aug. 6, 2020

Aug. 6, 2020

Hi all, I'm trying to use the 'density' method for the smooth() function (which points to the class SmoothedDensityEstimate), but I can't find any documentation about how to use the 'density' method of smooth (i.e. what fields, index fields, etc. I should feed it.) Could someone give me an example of how this method should be used? I'm using yt 3.6 with FLASH particle data. The link to the SmoothedDensityEstimate class code is https://github.com/yt-project/yt/blob/6befef2bc0427250fd62395962599be41b193…. Thanks, Camryn

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FLASH Nearest Neighbor - yt 3.6.0
by clp3ef＠virginia.edu Aug. 5, 2020

Aug. 5, 2020

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 Aug. 5, 2020

Aug. 5, 2020

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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