Mailman 3 August 2025 - yt-users

ANN: Grackle 3.4.1 and Gracklepy 1.2 Release
by Matthew Abruzzo Aug. 22, 2025

Aug. 22, 2025

We are pleased to announce the release of Grackle 3.4.1 and Gracklepy 1.2. Grackle is a library that provides chemistry and radiative cooling solver > for astrophysical simulations and models. Gracklepy provides python > bindings to the Grackle library. This release consists of 43 Pull Requests from 4 contributors (2 of them are first-time contributors). *Highlight: Releasing Gracklepy 1.2* The highlight of this announcement is the release of Gracklepy 1.2. Gracklepy was formerly known as Pygrackle, but the name has been changed in this release (to let us upload to PyPI). As of this release, you can now install Gracklepy from PyPI by invoking $ pip install gracklepy On most typical platforms, this will install precompiled wheels. On more exotic platforms, this will try to build Gracklepy from source. Please be aware that: 1. You should manually uninstall Pygrackle from your python environment (if its present) before you install Gracklepy 2. Gracklepy and Grackle rely upon data files for most use-cases. At this time, you will still need to manually download the data files yourself (but there are some pending pull requests that will change this in a future release) *List of All Changes:* *Bugfixes:* - Fix a significant oversight in *GrackleConfig.cmake* 330 <https://github.com/grackle-project/grackle/pull/330> - H2 self shielding length scale factor fix 325 <https://github.com/grackle-project/grackle/pull/325> - address a bug in *calc_temp_cloudy_g.F* 367 <https://github.com/grackle-project/grackle/pull/367> *Enhancements:* - Standard Status Reporting Machinery 269 <https://github.com/grackle-project/grackle/pull/269> - Remove pygrackle/api.py & pygrackle/utilities/api.py 352 <https://github.com/grackle-project/grackle/pull/352> - Rename pygrackle -> gracklepy (so we can upload to PyPI) 371 <https://github.com/grackle-project/grackle/pull/371> *Build-System:* - (core lib) introduce CMakePresets.json to enable compiler warnings in a CI job 334 <https://github.com/grackle-project/grackle/pull/334> - (core lib) Relocated all CMake dependency information into dependencies.cmake 296 <https://github.com/grackle-project/grackle/pull/296> - (core lib) assorted tweaks: 326 <https://github.com/grackle-project/grackle/pull/326> 329 <https://github.com/grackle-project/grackle/pull/329> 337 <https://github.com/grackle-project/grackle/pull/337> - (gracklepy) tweak cython handling 319 <https://github.com/grackle-project/grackle/pull/319> 328 <https://github.com/grackle-project/grackle/pull/328> - (gracklepy) Introduce dependency groups 347 <https://github.com/grackle-project/grackle/pull/347> *Testing:* - Support running subset of gracklepy test without an editable install 335 <https://github.com/grackle-project/grackle/pull/335> - Move test_chemistry_struct_synched between test suites 327 <https://github.com/grackle-project/grackle/pull/327> - * Fix a bug in *test_get_grackle_version.py* 390 <https://github.com/grackle-project/grackle/pull/390> *Documentation:* - gracklepy test instruction tweaks 309 <https://github.com/grackle-project/grackle/pull/309> - Assorted tweaks to appearance of doc website 285 <https://github.com/grackle-project/grackle/pull/285> 291 <https://github.com/grackle-project/grackle/pull/291> 346 <https://github.com/grackle-project/grackle/pull/346> - Fix spacing issues in docs 340 <https://github.com/grackle-project/grackle/pull/340> - Simplify GitHub hyperlinks for repository locations in docs 300 <https://github.com/grackle-project/grackle/pull/300> - Add more detail to gracklepy build documentation 294 <https://github.com/grackle-project/grackle/pull/294> - Added missing He 362 <https://github.com/grackle-project/grackle/pull/362> - Added chemistry network table 361 <https://github.com/grackle-project/grackle/pull/361> *Infrastructure:* - Optimize circleci workflows 338 <https://github.com/grackle-project/grackle/pull/338> - Introduce an extremely simplistic `.pre-commit-config.yaml` file 348 <https://github.com/grackle-project/grackle/pull/348> - Introduce GHA to upload Gracklepy wheels to PyPI 320 <https://github.com/grackle-project/grackle/pull/320> 355 <https://github.com/grackle-project/grackle/pull/355> 356 <https://github.com/grackle-project/grackle/pull/356> 389 <https://github.com/grackle-project/grackle/pull/389> - Bump versions of GHA action groups 360 <https://github.com/grackle-project/grackle/pull/360> 363 <https://github.com/grackle-project/grackle/pull/363> 365 <https://github.com/grackle-project/grackle/pull/365> 372 <https://github.com/grackle-project/grackle/pull/372> 373 <https://github.com/grackle-project/grackle/pull/373> - Move test-data retrieval logic into ``scripts/ci/fetch-test-data.py`` 307 <https://github.com/grackle-project/grackle/pull/307> - Address flake8 warnings (in files that it previously ignored) 368 <https://github.com/grackle-project/grackle/pull/368> 369 <https://github.com/grackle-project/grackle/pull/369> - Use builtin GitHub feature to nicely redirect to Code of Conduct 342 <https://github.com/grackle-project/grackle/pull/342> - Convert README.md to README.rst (and deduplicate content on the website landing page) 350 <https://github.com/grackle-project/grackle/pull/350> 351 <https://github.com/grackle-project/grackle/pull/351> *Contributors* - @brittonsmith <https://github.com/brittonsmith> - @KeiganM <https://github.com/KeiganM> (new!) - @mabruzzo <https://github.com/mabruzzo> - @mcsmithastro <https://github.com/mcsmithastro> (new!) *Grackle Advisory Council* - Matthew Abruzzo - Greg Bryan - Desika Narayanan - Marta Reina-Campos - Britton Smith - Matthew Turk *Full Changelog:* https://github.com/grackle-project/grackle/compare/grackle-3.4.0...grackle-…

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ANN: ytree 3.3 released
by Britton Smith Aug. 21, 2025

Aug. 21, 2025

Hi everyone! ytree 3.3 is released! ytree is an extension of yt for working with tree data and especially merger trees. This release contains several new features and minor enhancements, including improved support for the AHF format, support for generic tree data in CSV files, and improvements to the parallelism functionality. New Features - Add save_in_place option to save_arbor #139 <https://github.com/ytree-project/ytree/pull/139> - Add TreeContainer convenience class #140 <https://github.com/ytree-project/ytree/pull/140> - Add support for generic csv data #160 <https://github.com/ytree-project/ytree/pull/160> Minor Enhancements - Add ability to customize file naming conventions for AHF #172 <https://github.com/ytree-project/ytree/pull/172> - Add documentation for helpful attributes and make cosmology calculator a cached_property #175 <https://github.com/ytree-project/ytree/pull/175> - Add preprocess and handoff_attrs options to AnalysisPipeline #178 <https://github.com/ytree-project/ytree/pull/178> - Add automatic vector field detection #179 <https://github.com/ytree-project/ytree/pull/179> - Minor speedup for get_node #180 <https://github.com/ytree-project/ytree/pull/180> - Add nodes keyword to parallel_tree_nodes #181 <https://github.com/ytree-project/ytree/pull/181> - Parallelize get_nodes_from_selection #183 <https://github.com/ytree-project/ytree/pull/183> Bugfixes - Get correct file numbers when doing an update save #184 <https://github.com/ytree-project/ytree/pull/184> Infrastructure Updates - Replace deprecated unyt.uconcatenate function #165 <https://github.com/ytree-project/ytree/pull/165> - Updating python versions and fixing deprecations #167 <https://github.com/ytree-project/ytree/pull/167> - Update version support #169 <https://github.com/ytree-project/ytree/pull/169> - Replace setup.py with pyproject.toml #170 <https://github.com/ytree-project/ytree/pull/170> - Add resource_class for testing and remove daily tests #171 <https://github.com/ytree-project/ytree/pull/171> - Change deprecated numpy.in1d to isin #173 <https://github.com/ytree-project/ytree/pull/173> - Replace deprecated functions #174 <https://github.com/ytree-project/ytree/pull/174> - Generalize package description in docs #176 <https://github.com/ytree-project/ytree/pull/176> - Split frontend tests into separate files #177 <https://github.com/ytree-project/ytree/pull/177> ytree can be installed with pip or conda: pip install ytree conda install -c conda-forge ytree or update your existing installation: pip install --upgrade ytree conda update ytree Full documentation can be found at https://ytree.readthedocs.io/ Thanks as always to the wonderful yt community. Full Changelog: ytree-3.2.1...ytree-3.3.0 <https://github.com/ytree-project/ytree/compare/ytree-3.2.1...ytree-3.3.0>

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Smoothed_covering_grid and force_periodicity?
by dsmont80＠gmail.com Aug. 7, 2025

Aug. 7, 2025

Dear YT community and FLASH users, I am new to FLASH (running laserslab like problems in 2D Cylindrical symmetry) and new to YT. We have been using YT to read in FLASH hdf5 files from our 2D R-z laser simulations with cylindrical symmetry. We want to use smoothed_covering_grid to interpolate data to the highest resolution (highest refinement level). Following an example given on Scott Feister's GitHub page (https://github.com/sfeister/flsuite/blob/master/flsuite/flyt/flyt.py), if we use just “covering_grid” like his example, with arguments like he gives (max_level, left_edge, dims), things work well, but there is no interpolation, of course. However, if we simply switch to “smoothed_covering_grid” and then try to get out fields like dens, tele, etc., then we get the following error below. We take the advice in the error message and do: ds.force_periodicity() prior to pulling out the desired fields, and it “works”, but then at data boundaries (r=rmin, z=zmin, r=rmax, z=zmax) we get some funny wrap-around of the data due to the force_periodicity. Is there a way to avoid using "force_periodicity" with "smoothed_covering_grid"? We want the data interpolated to the finest AMR refinement level on a uniform 2D grid. Not sure why covering_grid works okay, but smoothed_covering_grid doesn’t on the same data set? The data are nicely interpolated everywhere except at the boundaries. Any help or advice would be appreciated. Thanks, David Montgomery **** error message we get below when trying something like Te = scg["tele"], where scg = ds.smoothed_covering_grid[max_level, left_edge, dims], where max_level = ds.max_level, left_edge = ds.domain_left_edge, and dims = ds.domain_dimensions * 2**np.array([max_level, max_level, 0]) **** Traceback (most recent call last): File "<python-input-24>", line 1, in <module> Te = scg["tele"] ~~~^^^^^^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/data_containers.py", line 235, in __getitem__ self.get_data(f) ~~~~~~~~~~~~~^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/construction_data_containers.py", line 915, in get_data self._fill_fields(fill) ~~~~~~~~~~~~~~~~~^^^^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/construction_data_containers.py", line 1494, in _fill_fields min_level = self._compute_minimum_level() File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/construction_data_containers.py", line 1478, in _compute_minimum_level for chunk in ils.data_source.chunks([], "io"): ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/selection_objects/data_selection_objects.py", line 94, in chunks self.get_data() # Ensure we have built ourselves ~~~~~~~~~~~~~^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/selection_objects/data_selection_objects.py", line 139, in get_data self.index._identify_base_chunk(self) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/geometry/grid_geometry_handler.py", line 332, in _identify_base_chunk gi = dobj.selector.select_grids( ^^^^^^^^^^^^^ File "/Users/david/Library/Python/3.13/lib/python/site-packages/yt/data_objects/selection_objects/data_selection_objects.py", line 89, in selector self._selector = sclass(self) ~~~~~~^^^^^^ File "yt/geometry/_selection_routines/region_selector.pxi", line 60, in yt.geometry.selection_routines.RegionSelector.__init__ RuntimeError: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0. Region left edge = -0.0006510416666666666 code_length, Region right edge = 0.25065104166666663 code_length Dataset left edge = 0.0 code_length, Dataset right edge = 0.25 code_length This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to select a smaller region that does not border domain edge (see https://yt-project.org/docs/analyzing/objects.html?highlight=region) or override the periodicity with ds.force_periodicity()

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Scaling Code Units to Physical Units while loading the data from HDF5
by Sumit Banerjee Aug. 1, 2025

Aug. 1, 2025

yt users, I am using FLASH for my simulations and I am working on the Sod problem as my entry point to my research. I have successfully completed simulating the Sod problem using cartesian grids in 3D. My simulation is in code units and I am trying to plot the output in physical units with length in parsecs and density in g/cc. I tried running FLASH with physical units but the values get very small and is not recommended. So, the only logical thing to do here is to somehow do this scaling when reading the data using yt.load(). Below is what I have done so far but the output plot is blank. # Example: define code units data.unit_registry.add('code_length', 3.086e18, dimensions = yt.units.dimensions.length) # 1 parsec data.unit_registry.add('code_mass', 1.989e33, dimensions = yt.units.dimensions.mass) # 1 solar mass data.unit_registry.add('code_time', 3.154e7, dimensions = yt.units.dimensions.time) # 1 year # Derived unit: velocity data.unit_registry.add('code_velocity', 1e5, dimensions = yt.units.dimensions.velocity) # 1 km/s # Extract the data in physical units data_physical = data.all_data() # Convert the physical quantities from code units to physical units density_cgs = data_physical["gas", "density"].to("g/cm**3") velocity_kms = data_physical["gas", "velocity_magnitude"].to("km/s") position_pc = data_physical["index", "x"].to("pc") # Plot the data yt.SlicePlot(data, "z", ("gas", "density"), center="c", width=(10, "pc")).show() Can you please help me converting the units from code units to physical units using yt? Clear Skies, Sam

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