Mailman 3 - yt-users

yt_idv 0.3.1
by Chris Havlin 17 Jun '23

17 Jun '23

Hello there, We're happy to announce that yt_idv (https://github.com/yt-project/yt_idv) version 0.3.1 is out. The 0.3 series includes a number of new features and fixes including the ability to now plot slices, isocontours and arbitrary curves! For full release notes, see v0.3.1 <https://github.com/yt-project/yt_idv/releases/tag/v0.3.1> and v0.3.0 <https://github.com/yt-project/yt_idv/releases/tag/v0.3.0>. Take it for a spin and let us know if you have any problems (open an issue <https://github.com/yt-project/yt_idv/issues/new> or reach on on the yt slack)! Best, Chris Havlin

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What's up in yt for June 2023
by Matthew Turk 08 Jun '23

08 Jun '23

Hi everyone! We're trying something new -- there's a lot going on in the yt community, and we wanted to tell you about some of it. ## yt 4.2 As you may have seen recently, yt 4.2 was released at the end of May: https://github.com/yt-project/yt/releases/tag/yt-4.2.0 Many, *many* thanks to Clément Robert for pushing forward so much of this release. It includes a number of enhancements, but perhaps one of the most important is a major improvement to how yt stores and handles index files for particle datasets. This work was a collaboration including John ZuHone and Kacper Kowalik. We also want to take this opportunity to remind folks that yt development can be community-driven -- which means sharing with us feedback, thoughts on what can be improved, and even chipping in to help out with code, documentation, and even just talking about what you do with yt on Slack or over email -- see the bottom of this message for more! We have a list of fun, introductory issues for new contributors: https://github.com/yt-project/yt/labels/new%20contributor%20friendly and some we're looking for help with: https://github.com/yt-project/yt/labels/help%20wanted ## Workshop Presentations In April, we had an informal online workshop. The videos from that are now online and we invite you to check them out -- they cover an introduction to using yt and some of the basics of how to get started analyzing data. Day One: https://www.youtube.com/watch?v=h6NE32WagHs Day Two: https://www.youtube.com/watch?v=fn45FK7hX7Q Matt also streams development once in a while at twitch.tv/powersoffour , but be sure to manage your expectations on that front! ## Widgyts for Jupyter and yt One of the yt family of projects, Widgyts (https://widgyts.readthedocs.org/ and github.com/yt-project/widgyts ) just had another release in early April. Widgyts, as the *extremely* clever name suggests, is widgets for yt within Jupyter and Jupyterlab. The new version includes a mesh viewer for finite element meshes, as well as preliminary support for displaying particles in the viewer. If you're using AMR datasets or FEM, check it out! ## Libyt Shin-Rong Tsai and Hsi-Yu Schive are in the final stages of preparing the library 'libyt' for release, with initial connections to the GAMER code and Enzo. libyt is an in-situ analysis library that provides the ability to execute analysis and visualization during the course of large-scale computations. Look for more information soon, but the code is currently available at github.com/calab-ntu/libyt , and Shin-Rong will be giving a talk at Scipy 2023 about libyt. ## Scipy 2023 At Scipy 2023 this year, there will be two presentations about yt or yt-related projects. The first, from Chris Havlin, will be on July 13 at 3PM in Grand Salon C, in the "Earth, Ocean, Geo, and Atmospheric" track, on `yt_xarray`: https://cfp.scipy.org/2023/talk/QYHD3G/ The second, from Shin-Rong Tsai, will be on July 12 at 1:55PM in Grand Salon C, in the "Astronomy and Physics" track, on `libyt`: https://cfp.scipy.org/2023/talk/JTXC9W/ If you're at SciPy, come see them and say hi! Usually all the talks are recorded, and we'll be sure to include them in a future newsletter. ## Slack As a reminder, we have a Slack community where you can ask questions, suggest things for development, or just generally chat. You can join by visiting https://yt-project.org/slack.html . ## Tell Us About Your Stuff! We'd love to share news of your papers in our next newsletter -- so please reach out to matthewturk(a)gmail.com to share when you publish a paper that uses yt you'd like to have shared out. Even if you don't want us to include it in a newsletter, we still like to hear about them! And we would also *love* to have new blog posts for https://blog.yt-project.org/ , which Madicken Munk set up with a really cool autodeployment system -- you just need to make an issue in the repository (https://github.com/yt-project/blog ) to contribute an article! (for more info: https://yt-project.github.io/blog/posts/contributing/ ) That's all for now, folks -- happy computing!

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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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Fwd: ANN: Grackle 3.2 released!
by Britton Smith 22 May '23

22 May '23

---------- Forwarded message --------- From: Matthew Abruzzo <matthewabruzzo(a)gmail.com> Date: Mon, May 22, 2023 at 3:31 PM Subject: ANN: Grackle 3.2 released! To: <grackle-cooling-users(a)googlegroups.com> Grackle 3.2 is released! Grackle is a chemistry and radiative cooling solver for astrophysical simulations and models. The Grackle 3.2 release consists of 75 pull requests from 13 contributors, 8 of them new to the project. It contains 7 new features, 14 minor enhancements, 15 bugfixes, and significantly enhanced documentation. 8 functions have also been deprecated and will be removed in the future. See below for further details. This also marks the official release of Pygrackle 1.0. Pygrackle is the Python interface to Grackle. Pygrackle has been a part of Grackle since the beginning, but from this point on it will be properly versioned. *New Features* * Enhanced dust treatment #43 <https://github.com/grackle-project/grackle/pull/43>, #94 <https://github.com/grackle-project/grackle/pull/94> * Use Grackle in yt fields #62 <https://github.com/grackle-project/grackle/pull/62> * New high density cooling table #71 <https://github.com/grackle-project/grackle/pull/71> * Callable functions for all reaction rates #87 <https://github.com/grackle-project/grackle/pull/87> * New get_velocity_units and get_temperature_units functions #97 <https://github.com/grackle-project/grackle/pull/97>, #96 <https://github.com/grackle-project/grackle/pull/96> * Updated H2 self-shielding (reissue of PR #72) #98 <https://github.com/grackle-project/grackle/pull/98> * New dynamic API #130 <https://github.com/grackle-project/grackle/pull/130>, #141 <https://github.com/grackle-project/grackle/pull/141> *Minor Enhancements* * Use gamma in mean molecular weight. #65 <https://github.com/grackle-project/grackle/pull/65> * Add ability to query the Grackle Version #109 <https://github.com/grackle-project/grackle/pull/109> * Embed compiled precision into grackle header. #118 <https://github.com/grackle-project/grackle/pull/118> * Convert iteration limit to a runtime parameter #124 <https://github.com/grackle-project/grackle/pull/124> * Pygrackle mu improvements #54 <https://github.com/grackle-project/grackle/pull/54> * Change redshift interpolation to log(1+z) #126 <https://github.com/grackle-project/grackle/pull/126> * Significant Pygrackle refactor #88 <https://github.com/grackle-project/grackle/pull/88>, #140 <https://github.com/grackle-project/grackle/pull/140> * Add updated H2-H rate based on Lique (2015) #61 <https://github.com/grackle-project/grackle/pull/61> * Add test of synchronization between chemistry_data and dynamic API. #136 <https://github.com/grackle-project/grackle/pull/136> * Modified the chemistry_data struct so that the omp_nthreads is always a field #148 <https://github.com/grackle-project/grackle/pull/148> * Add machine file for tigercpu at Princeton #74 <https://github.com/grackle-project/grackle/pull/74> * MacOS Big Sur makefile #84 <https://github.com/grackle-project/grackle/pull/84> * Updating makefiles for NASA's HECC machines #86 <https://github.com/grackle-project/grackle/pull/86> * Updates for Stampede Builds #58 <https://github.com/grackle-project/grackle/pull/58> *Bugfixes* * Mmw bugfix #79 <https://github.com/grackle-project/grackle/pull/79> * fix energy and pressure units in pygrackle #49 <https://github.com/grackle-project/grackle/pull/49> * Update cool1d_multi_g.F #59 <https://github.com/grackle-project/grackle/pull/59> * Fixing lifetime issue for grackle_data_path in the Cython Grackle wrapper #80 <https://github.com/grackle-project/grackle/pull/80> * Fix velocity_units in freefall.py #92 <https://github.com/grackle-project/grackle/pull/92> * fix internal velocity units #97 <https://github.com/grackle-project/grackle/pull/97> * Fix line length issues #102 <https://github.com/grackle-project/grackle/pull/102> * Avoid use of uninitialized variables when setting the timestep in dense gas #103 <https://github.com/grackle-project/grackle/pull/103> * Modify property calculations to respect grid_start and grid_stop #106 <https://github.com/grackle-project/grackle/pull/106> * provide sensible version info without git #114 <https://github.com/grackle-project/grackle/pull/114> * Change get_grackle_version to explicitly accept zero arguments. #115 <https://github.com/grackle-project/grackle/pull/115> * Changing _inner_range to static inline to avoid undefined reference #117 <https://github.com/grackle-project/grackle/pull/117> * Remove duplicate precision definition during compile #137 <https://github.com/grackle-project/grackle/pull/137> * Changed the type of chemistry_data's grackle_data_file field from char* to const char* #147 <https://github.com/grackle-project/grackle/pull/147> * fix oversight where some dynamic API functions initially had size_t in their signature & necessitated inclusion of <stddef.h> #144 <https://github.com/grackle-project/grackle/pull/144>, #149 <https://github.com/grackle-project/grackle/pull/149> * Bugfix: making inline legacy internal grackle functions work in C codes #157 <https://github.com/grackle-project/grackle/pull/157> *Documentation Updates* * Update comment #52 <https://github.com/grackle-project/grackle/pull/52> * Add instructions for how to initialize data submodule. #82 <https://github.com/grackle-project/grackle/pull/82> * Updated Documentation #90 <https://github.com/grackle-project/grackle/pull/90> * Expand units documentation and remove ceiling on metal density #121 <https://github.com/grackle-project/grackle/pull/121> * Document optimization issues in Fortran example with gfortran 9.2.1 & 9.4.0 #125 <https://github.com/grackle-project/grackle/pull/125> * Add warnings about compiling in single precision. #120 <https://github.com/grackle-project/grackle/pull/120> * Add documentation for CaseBRecombination parameter. #122 <https://github.com/grackle-project/grackle/pull/122> * Add clarification to docs on electron density. #131 <https://github.com/grackle-project/grackle/pull/131> * documentation fixes for later sphinx versions #132 <https://github.com/grackle-project/grackle/pull/132> * Expand discussion in documentation of cooling units. #154 <https://github.com/grackle-project/grackle/pull/154> * Add warning about self-shielding cooling tables. #155 <https://github.com/grackle-project/grackle/pull/155> *Infrastructure Updates* * Switch from csh to bash in configure. #47 <https://github.com/grackle-project/grackle/pull/47> * add data files as submodule #75 <https://github.com/grackle-project/grackle/pull/75> * Update pygrackle version to 1.0.0 and add metadata. #151 <https://github.com/grackle-project/grackle/pull/151> *Deprecations* The following functions have been deprecated and will be removed in the next feature release. * Functions taking all field arrays as arguments (starting in "_") #44 <https://github.com/grackle-project/grackle/pull/44> * _solve_chemistry * _calculate_cooling_time * _calculate_gamma * _calculate_pressure * _calculate_temperature * Remaining functions starting with "_" #139 <https://github.com/grackle-project/grackle/pull/139> * _set_default_chemistry_parameters (renamed local_initialize_chemistry_parameters) * _initialize_chemistry_data (renamed local_initialize_chemistry_data) * _free_chemistry_data (renaned local_free_chemistry_data) * free_chemistry_data added to free structures in grackle.h *Contributors* * Avi Friedlander (new!) * Ben Wibking (new!) * Britton Smith * Claire Kopenhafer (new!) * Ewan Jones (new!) * He Jia (new!) * John Wise * Leonard Romano (new!) * Loic Hausammann * Matthew Abruzzo (new!) * Molly Peeples * Simon Glover * Weiguang Cui (new!) *Grackle Advisory Council* * Greg Bryan * Desika Narayanan * Marta Reina-Campos * Britton Smith * Matthew Turk *Full Changelog*: https://github.com/grackle-project/grackle/commits/grackle-3.2.0 -- You received this message because you are subscribed to the Google Groups "Grackle Cooling Library Users" group. To unsubscribe from this group and stop receiving emails from it, send an email to grackle-cooling-users+unsubscribe(a)googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/grackle-cooling-users/CACMuPYBZyAFJeFCU%3… <https://groups.google.com/d/msgid/grackle-cooling-users/CACMuPYBZyAFJeFCU%3…> .

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YT and ANSYS Fluent
by sjessin7＠gmail.com 17 May '23

17 May '23

Hey guys, just wanted to ask if someone got experience in loading results from Fluent with yt. I only got errors when trying to load the dat.h5 files saying missing "keys" while loading database.

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NAN occurs when calculating second-order gradient fields
by hyf＠stu.pku.edu.cn 10 May '23

10 May '23

Hi everyone， I have tried to use the function 'add_gradient_fields' to calculate the second-order derivative of density 'rho' with x-direction, i.e., 'rho_gradient_x_gradient_x'. Here is the code: rho_gradientx = ds.add_gradient_fields(('boxlib','rho')) ds.periodicity = (True, True, True) rho_gradientxx = ds.add_gradient_fields(('boxlib','rho_gradient_x')) Unfortunately, nan occurs when I tried to plot the field 'rho_gradient_x_gradient_x' I will be appreciate if anyone can give me suggestions about how to fix it or provide other solutions to calculate higher order(more than 1st order) gradient fields. Best wishes, He Yifeng

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Splitting ewah_bool_utils
by Matthew Turk 08 May '23

08 May '23

Hi folks, Just a heads up that we're going to merge https://github.com/yt-project/yt/pull/2711 soon. This takes some code that was yt specific and moves it to an external package (where perhaps it can find use outside of yt). The only impact this will have is if you are accustomed to installing yt from source, where you will now need to also have this installed. If you are used to using yt from conda, pip, etc, then the dependency resolution will pick up the change and install it. *But*, if you are installing yt from source, you'll also need to install 'ewah_bool_utils' which is located at: https://github.com/yt-project/ewah_bool_utils , as well as on conda-forge, pypi, etc. -Matt

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calculate the mass flux in yt
by Jingyao Zhu 27 Apr '23

27 Apr '23

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 25 Apr '23

25 Apr '23

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 11 Apr '23

11 Apr '23

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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