Mailman 3 July 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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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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Struggling to use LinePlot with GADGET-4 data
by christianvdm＠saao.ac.za 10 Aug '22

10 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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Enzo-E v1.0 Announcement
by Matthew William Abruzzo 02 Jul '22

02 Jul '22

We are pleased to announce the v1.0 release of Enzo-E, a new parallel adaptive mesh refinement magnetohydrodynamics code. Enzo-E is based on Cello, a highly scalable, fully-distributed array-of-octree parallel adaptive mesh refinement (AMR) framework, and Enzo-E is a scalable branch of the original Enzo parallel astrophysics and cosmology application that has been ported to use Cello. Enzo-E’s parallel scalability is enabled by Charm++ (https://charmplusplus.org/), an advanced parallel runtime system developed at the University of Illinois. A short paper describing Enzo-E can be found here <https://ui.adsabs.harvard.edu/abs/2018arXiv181001319B/abstract>. Features include: - Three HD/MHD solvers: PPM, PPML, VL+CT - Self gravity with a multigrid Poisson solver - Collisionless particles - Cosmological evolution - A wide range of star formation and sink algorithms - Scalable HDF I/O - Radiative cooling and chemistry via connection to the Grackle package Source code repository: https://github.com/enzo-project/enzo-e Documentation: http://enzo-e.readthedocs.io/ Cello was written by James Bordner and Enzo-E includes contributions from: Matthew Abruzzo Stefan Arridge James Bordner Thomas Bolden Greg Bryan Vanesa Diaz Andrew Emerick Forrest Glines Ryan Golant Nathan Goldbaum Buket Benek Gursoy Philipp Grete William Hicks Michael Norman Claire Kopenhafer Brian O’Shea Molly Peeples John Regan Dan Reynolds Wolfram Schmidt Britton Smith Jason Tumlinson Matthew Turk Saoirse Ward Sophie Wenzel-Teuber John Wise Enzo-E / Cello has benefitted from the following funding sources in reverse chronological order. - NASA TCAN 80NSSC21K1053 (PI: Peeples; Co-PIs: Bryan, Norman, O’Shea, Wise) - Irish Research Council New Foundations Scheme (2019; PI: Regan) - NSF OAC-1835402 (PI: Norman; Institutional PIs: Bryan, O’Shea, Wise) - NSF SI2 SSE-1440709 (PI: Norman) - NSF PHY-1104819 (PI: Norman) - NSF AST-0808184 (PI: Norman)

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