Mailman 3 April 2023 - yt-users

enzo-mrp-music/get_halo_initial_extent.py not working with yt 4.0.1
by C Bernhardt June 2, 2023

June 2, 2023

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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calculate the mass flux in yt
by Jingyao Zhu April 27, 2023

April 27, 2023

Dear all, I have a question on calculating the mass flux across surfaces in yt, particularly why the flux values differ between two methods. The surface, for example, is a circle a few kpcs above the central XY plane, and I'm calculating the mass flux in the perpendicular (velocity_z) direction. A simplified code snippet looks like this. ds = yt.load('Enzo_AMR_output') box_length_kpc = ds.domain_width[0].in_units('kpc').value # constant, simulation box length in kpc *Method 1.* Create a 2D yt.slice object and calculate the flux manually (faster). slice = ds.r[:, :, 0.5 + 2/box_length_kpc] # selecting a slice at z=2 kpc (relative to domain center) # creating a boolean mask: a circle with a radius of 10 kpc radius_mask = np.sqrt((slice['gas','x'].in_units("kpc").value-box_length_kpc/2.)**2 +\ (slice_plus['gas','y'].in_units("kpc").value-box_length_kpc/2.)**2) <= 10 # mdot = rho * v dot dA, where dA = dx * dy mass_flux = np.sum((slice['gas', 'density'][radius_mask_] *\ slice['gas', 'velocity_z'][radius_mask] *\ slice['gas', 'dx'][radius_mask] *\ slice['gas', 'dy'][radius_mask])).in_units("Msun/yr") *Method 2.* Create a yt.surface object and use the calculate_flux() function. # defining a disk object of radius 10 kpc, then selecting the upper surface where z=2 kpc (relative to domain center), and calculate the mass flux my_disk = ds.disk(ds.domain_center, [0.0, 0.0, 1.0], 10 * kpc, 2.02 * kpc) disk_upper_surf = ds.surface(my_disk, ("gas", "cylindrical_z"), 2) mass_flux = disk_upper_surf.calculate_flux(("gas", "velocity_x"),("gas", "velocity_y"),("gas", "velocity_z"),("gas", "density")).in_units("Msun/yr") The two methods always return different results (off by ~48% for this selected input), but I wonder why. Another sanity check I did was to print out the cell numbers selected in each method. Method 2 (marching cubes, triangular vertices) consistently selected 2 times the cell numbers in method 1 (slicing). Could anyone point out what might be wrong with the way I implemented either method? Thanks so much! Best, Jingyao -- Jingyao Zhu (she/her/hers) Columbia University | Dept of Astronomy

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pyxsim Installation problems using conda
by Micheli Moura April 25, 2023

April 25, 2023

Hello, I am having some trouble trying to install pyxsim on JupiterLab from Illustris workspace. I started with YT install using pip and then I've tried to install pyxsim using pip as well, but "Could not find a version that satisfies the requirement yt>=4.1.3 (from pyxsim) [...] No matching distribution found for yt>=4.1.3 (from pyxsim). Then I tried to install via conda, but "PackagesNotFoundError: The following packages are not available from current channels: - pyxsim. And the installation method from source returns the same error from pip. Seems like this bug report: https://github.com/jzuhone/pyxsim/issues/42, but I installed the unyt module and the errors still there... There is something I can do to fix it?

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ANN: Virtual short-form course on using yt the week of April 10, 2023
by Matthew Turk April 11, 2023

April 11, 2023

Hi all, I'm writing to announce that the week of April 10, we'll have a short-form course streamed online on how to use yt. It will be live broadcast through Twitch and later uploaded to YouTube for on-demand viewing. The presentations will be staggered across several different times-of-day to accommodate viewers in different time zones and will initially cover materials drawn from the "yt Quickstart" notebooks, building to an in-depth exploration of a dataset. Each day will include time for Q&A and interactive discussions. The times for the workshop will be: - Monday, April 10: 12:00-14:00 CDT / 17:00-19:00 UTC - Tuesday the 11th: 8:30-10:30 CDT / 13:30-15:30 UTC - Wednesday the 12th, 15:00-17:00 CDT / 20:00-22:00 UTC - Thursday the 13th, 11:00-13:00 CDT / 16:00-18:00 UTC In the days leading up to the workshop I will post here with more information about joining the live stream, as well as a rough breakdown of what topics will be covered on which days. Best, Matt

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