Mailman 3 May 2023 - 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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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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