Mailman 3 August 2022 - yt-users

enzo-mrp-music/get_halo_initial_extent.py not working with yt 4.0.1
by C Bernhardt 02 Jun '23

02 Jun '23

Dear yt users, I just updated yt to 4.0.1 and now I get this error message when trying to run enzo-mrp-music.py from John Wise on https://github.com/jwise77/enzo-mrp-music. Traceback (most recent call last): File "enzo-mrp-music/enzo-mrp-music.py", line 264, in <module> params = find_lagrangian_region(params) File "enzo-mrp-music/enzo-mrp-music.py", line 177, in find_lagrangian_region get_center_and_extent(params["halo_info"], File "enzo-mrp-music/get_halo_initial_extent.py", line 147, in get_center_and_extent halo_indices, halo_com, shifted = get_halo_indices(my_halo, final_dataset, File "enzo-mrp-music/get_halo_initial_extent.py", line 119, in get_halo_indices get_halo_sphere_particles(my_halo, dataset, radius_factor=radius_factor) File "enzo-mrp-music/get_halo_initial_extent.py", line 73, in get_halo_sphere_particles my_sphere = pf.h.sphere(my_halo_data['center'], radius_factor * r_200) AttributeError: 'EnzoDataset' object has no attribute 'h' I am honestly not sure what the attribute 'h' does in this case, so I didn't know what to try to adjust. Any suggestions for getting around this? Or how can I go back to yt 3? Kind regards, -- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik

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ANN: yt 4.0.5 is out
by Clément Robert 25 Aug '22

25 Aug '22

Fresh bugfix batch is out of the oven: announcing yt 4.0.5 ! We strongly recommend upgrading if you're using yt to analyse SPH data. See the release notes for details https://github.com/yt-project/yt/releases/tag/yt-4.0.5 Happy analysis ! Clément

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ANN: Trident 1.3 released!
by Cameron Hummels 23 Aug '22

23 Aug '22

Hey everyone, I'm pleased to announce the release of Trident version 1.3! Trident is an extension of yt for creating absorption spectra from simulations and post-processing datasets to account for ionic species. Trident 1.3 brings Trident up to speed with yt 4, with all of its support for particle-based datasets and speed improvements in LightRay and spectral generation. This release also fixes some of the recent bugs that have crept in preventing the stable version of trident to load in some circumstances. The latest version of Trident can be installed with pip: pip install trident Documentation: https://trident.readthedocs.io/en/latest/ Repository: https://github.com/trident-project/trident Trident has received contributions from 25 people. Thanks to everyone for their hard work! - Trident development team Brendan Boyd Iryna Butsky Lauren Corlies Bili Dong Hilary Egan Nathan Goldbaum Zach Hafen Cameron Hummels Bharat Kambalur BW Keller Kacper Kowalik Erwin Lau Andrew Myers Molly S. Peeples Douglas Rudd Anthony Scopatz Devin Silvia Stephen Skory Britton Smith Clayton Strawn Stephanie Tonnesen Matthew Turk Miguel de Val-Borro John Wise John ZuHone -- Cameron Hummels Computational Astrophysicist California Institute of Technology http://chummels.org

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Multipanel plot with multi-column
by HyeonYong Kim 22 Aug '22

22 Aug '22

Hi all, I've used AxesGrid to draw a multipanel plot, and it properly worked. But now, I want to make a multipanel plot with a multicolumn like this. First row - 3 plots Second row - 4 plots Third row - 3 plots I looked at the document of AxesGrid but it seems that it only supports uniform grid structure (ex. 2x5, 3x3) And I also tried to use fixed resolution buffer to transform dataset to array, but it doesn't work ``` p = yt.ParticleProjectionPlot(ds,'z', (dm_f, 'particle_mass') ,width = (1200, "kpccm"),center=cen, density=True) p.data_source.to_frb((size, "kpccm"), 1024) >>> 'ParticleAxisAlignedDummyDataSource' object has no attribute 'to_frb' ``` Is there any way to draw a multicolumn plot like this link? (https://matplotlib.org/stable/gallery/subplots_axes_and_figures/gridspec_mu…) I would appreciate it if anyone can give me some hints. Thank you for reading! Sincerely, HyeonYong

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How to obtain the coordinates of the highest density countour
by Guido Granda Muñoz 22 Aug '22

22 Aug '22

Hello, I'm trying to obtain the coordinates of the highest density contour level in a region of a simulation. The code I'm using is the following: import yt from yt.units import * loc='/fs/san11/enro/guido/cflows_gg/fixed_mesh_l9_supersonic/' basename='cflows_gg_hdf5_plt_cnt_' out_name='reg1_cg_lines_start_points' n_s=10 n_e=10 d_n=1 nlines=7 # number of lines per plane dimension ## region ## # region 1 # xc=0.0 yc=1.0 zc=4.3 lx=3.0 ly=2.0 lz=2.0 center_r=[xc,yc,zc]*pc left_r =[xc-lx,yc-ly,zc-lz]*pc right_r =[xc+lx,yc+ly,zc+lz]*pc #### connected sets ### levels=3 for i in range(n_s,n_e+1,d_n): print('i: {}'.format(i)) ds=yt.load(loc+basename+str(i).zfill(4)) reg=ds.region(center_r,left_r,right_r) reg_max_rho=reg[('gas','density')].max() reg_min_rho=reg[('gas','density')].min() print("Density : [{0:.4e},{1:.4e}]".format(reg_max_rho,reg_min_rho)) contour_values, connected_sets=reg.extract_connected_sets(('gas','density'),levels,reg_min_rho*100,reg_max_rho,) #print("contour_values: {}".format(contour_values)) So, I wonder if the way to obtain the coordinates that I need is with: connected_sets[levels-1][1].fcoords This is what I obtained: unyt_array([[ 4.82137180e+16, -2.45889962e+18, 7.37669886e+18], [ 4.82137180e+16, -2.45889962e+18, 7.47312629e+18], [ 1.44641154e+17, -2.55532706e+18, 7.18384399e+18], [ 1.44641154e+17, -2.55532706e+18, 7.37669886e+18], [ 1.44641154e+17, -2.45889962e+18, 7.28027142e+18]], 'code_length') This is a (5,3) array, why it has that shape ?? Thanks,

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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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MemoryError when use the yt_SlicePlot function
by hyf＠stu.pku.edu.cn 10 Aug '22

10 Aug '22

Hi everyone, I met a trouble when I use the yt_SlicePlot function to plot a figure. It shows that --------------------------------------------------------------------------------------------------------------------- MemoryError: Unable to allocate 3.00 GiB for an array with shape (134217728, 3) and data type float64 ------------------------------------------------------------------------------------------------------------------ and seems that the array used to plot a figure is too large. I will appreciate that if anyone can give me some help! Best wishes, He Yifeng

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Struggling to use LinePlot with GADGET-4 data
by christianvdm＠saao.ac.za 09 Aug '22

09 Aug '22

Hi all, I am very new to YT and I have been trying to create a line plot for my GADGET-4 simulation output, but I keep running into a problem. I try to do a similar plot as that found here: https://yt-project.org/doc/cookbook/simple_plots.html#simple-1d-line-plotti…. I want to be able to 'draw' an arbitrary line and see how a quantity such as density changes along that line. My script and an example snapshot is linked below with the error I am getting following after. The code: http://paste.yt-project.org/show/392/ The snapshot and code: http://use.yt/upload/6dd0e0b8 YT version: 4.0.4 I keep getting this traceback error: " Traceback (most recent call last): File ~/PATH/yt_analysis.py:85 in <module> plot = yt.LinePlot(ds, "Density", (0.0, 0.0, 0.0), (0.0, 1.0, 0.0), 1000) File ~/.local/lib/python3.9/site-packages/yt/visualization/line_plot.py:174 in __init__ self._setup_plots() File ~/.local/lib/python3.9/site-packages/yt/visualization/line_plot.py:308 in _setup_plots x, y = self.ds.coordinates.pixelize_line( File ~/.local/lib/python3.9/site-packages/yt/geometry/coordinates/cartesian_coordinates.py:284 in pixelize_line arc_length, plot_values = _sample_ray(ray, npoints, field) File ~/.local/lib/python3.9/site-packages/yt/geometry/coordinates/cartesian_coordinates.py:47 in _sample_ray ray_coordinates = uvstack([ray[("index", d)] for d in "xyz"]).T File ~/.local/lib/python3.9/site-packages/yt/geometry/coordinates/cartesian_coordinates.py:47 in <listcomp> ray_coordinates = uvstack([ray[("index", d)] for d in "xyz"]).T File ~/.local/lib/python3.9/site-packages/yt/data_objects/data_containers.py:258 in __getitem__ self.get_data(f) File ~/.local/lib/python3.9/site-packages/yt/data_objects/selection_objects/data_selection_objects.py:211 in get_data self._generate_fields(fields_to_generate) File ~/.local/lib/python3.9/site-packages/yt/data_objects/selection_objects/data_selection_objects.py:232 in _generate_fields fd = self._generate_field(field) File ~/.local/lib/python3.9/site-packages/yt/data_objects/data_containers.py:299 in _generate_field tr = self._generate_fluid_field(field) File ~/.local/lib/python3.9/site-packages/yt/data_objects/data_containers.py:318 in _generate_fluid_field rv = finfo(gen_obj) File ~/.local/lib/python3.9/site-packages/yt/fields/derived_field.py:294 in __call__ dd = self._function(self, data) File ~/.local/lib/python3.9/site-packages/yt/geometry/coordinates/coordinate_handler.py:24 in _coords rv = data.ds.arr(data.fcoords[..., axi].copy(), units) File ~/.local/lib/python3.9/site-packages/yt/data_objects/selection_objects/data_selection_objects.py:418 in fcoords return self._current_chunk.fcoords File ~/.local/lib/python3.9/site-packages/yt/geometry/geometry_handler.py:255 in cached_func tr = self._accumulate_values(n[1:]) File ~/.local/lib/python3.9/site-packages/yt/geometry/geometry_handler.py:292 in _accumulate_values arrs.append(f(self.dobj)) File ~/.local/lib/python3.9/site-packages/yt/data_objects/index_subobjects/particle_container.py:17 in _func_non_indexed raise YTNonIndexedDataContainer(self) YTNonIndexedDataContainer: The data container (<class 'yt.data_objects.index_subobjects.particle_container.ParticleContainer'>) is an unindexed type. Operations such as ires, icoords, fcoords and fwidth will not work on it." Help with this would be highly appreciated. Kind regards, Christian

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