Mailman 3 December 2021 - 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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Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 15, 2022

Aug. 15, 2022

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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Clump Finding for Gadget2 format
by 201s408s＠stu.kobe-u.ac.jp Feb. 21, 2022

Feb. 21, 2022

Dear all, For my master's research, I installed yt and I want to load my research data converted to gadget2 format with yt. The function I want to use is the clump function, and I want to create a similar figure by performing the same processing as the Clump Finding below. https://yt-project.org/doc/cookbook/constructing_data_objects.html#cookbook… First of all, I tried to test with the gadget data placed in the data index, but neither the default nor the hdf5 format works. Is it possible to do Clump Finding in Gadget2 format?

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Error when attempting plot derived_fields quantities
by 贺一峰 Jan. 27, 2022

Jan. 27, 2022

Hi all, I have been trying to plot derived field of vorticity and the computation domain is set to be periodic. It always does not work though I tried to adjust different plotting domains. Meanwhile it can plot field figures of primitive quantities. Here is part of error info: ---------ERROR INFO----------------------------------------------------------------------------------------- P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: current_time = 3e-06 P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: domain_dimensions = [1024 128 1] P001 yt : [INFO ] 2021-10-06 19:50:59,037 Parameters: domain_left_edge = [0. 0. 0.] P001 yt : [INFO ] 2021-10-06 19:50:59,038 Parameters: domain_right_edge = [0.032 0.004 1. ] command in line argument loading data File "vorfield.py", line 76, in <module> slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((0.016,'cm'),(0.002,'cm')),center=([0.016,0.002,0.],'cm')) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__ slc.get_data(fields) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data self._generate_fields(fields_to_generate) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields fd = self._generate_field(field) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field tr = self._generate_fluid_field(field) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__ self.get_data(f) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data if len(fill) > 0: self._fill_fields(fill) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1053, in _fill_fields for chunk in ls.data_source.chunks(fields, "io"): File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1464, in chunks self.get_data() # Ensure we have built ourselves File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1507, in get_data self.index._identify_base_chunk(self) File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/geometry/grid_geometry_handler.py", line 290, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1459, in selector self._selector = sclass(self) File "yt/geometry/selection_routines.pyx", line 860, in yt.geometry.selection_routines.RegionSelector.__init__ RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 2. Region left edge = -1.25 code_length, Region right edge = 2.25 code_length Dataset left edge = 0.0 code_length, Dataset right edge = 1.0 code_length This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller region that does not border the edge or override the periodicity for this dataset. ---------ERROR INFO---------------------------------------------------------------------------------------- Here is part of python code ----------PYCODE--------------------------- ### u,v means velocity(primitive quantities) in X,Y direction ### vort_z means vorticity(derived quantity) in Z direnction def vort_z_func(field, data): return ( + data['boxlib', 'v_gradient_x'] - data['boxlib', 'u_gradient_y'] ) u_gradient = ds.add_gradient_fields(("boxlib","u")) v_gradient = ds.add_gradient_fields(("boxlib","v")) derived_fields = [ # field name, units, displayname ('vort_z', '1 / cm', 'Vorticity in z direction'), ] for name, unitstr, dispname in derived_fields: ds.add_field( ('boxlib', name), units = unitstr, function = eval(name + '_func'), sampling_type = 'cell', display_name = dispname ) slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((0.016,'cm'),(0.002,'cm')),center=([0.016,0.002,0.],'cm')) ----------PYCODE--------------------------- Thanks a lot! Best Wishes, He Yifeng College of Engineering, Peking University

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Re: Clump Finding for Gadget2 format
by Tomoyuki Shiokawa Dec. 22, 2021

Dec. 22, 2021

Hi Mr. Smith , Thank you very much for your prompt reply. As instructed, I changed my own environment (anaconda) and executed it with the latest yt ( yt 4.0.1 py310hb5077e9_1 conda-forge), referring to the following URL. https://yt-project.org/docs/dev/installing.html However, the error did not improve and I got the same one.... If you have anything else to try, please let me know. Tomoyuki

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Rockstar still doesn't work from yt
by kevin.lo＠ed.ac.uk Dec. 17, 2021

Dec. 17, 2021

The rockstar halo finder in yt_astro_analysis doesn't work in the newest version of yt. It had worked on the previous version of yt on cuillin, but since this morning it has stopped working. The error message is RuntimeError: Particle type (filter) PartType1 not found. But PartType1 definitely exists in the target file. Was the fix from the cuillin version not carried forward?

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Extracting 3D data and position values
by hdav7324＠uni.sydney.edu.au Dec. 16, 2021

Dec. 16, 2021

Hi all, I'm using yt to extract 3D data from a Ramses simulation cube. Specifically, I want to extract ("gas", "velocity_x") values from a smaller region within the cube. After this, I need to generate a set of (x,y,z) coordinates that correspond to the positions of those data values. So far I have tried doing this with ds.r and meshgrid (my code is given below). However, I'm uncertain if the ordering of my x,y,z coordinates matches the ordering of the data values? Is this the best method to do this? I question whether I should be using covering_grid instead, but am struggling to figure out how to use covering_grid to select out data for only a specific region within the simulation (the sim seems to extend between -300 to 300kpc in all dimensions, but I only want data between -15 to 15 kpc in all dimensions) Thanks for any help! Here is my code: sl = ds.r[(285, 'kpc'):(315, 'kpc'):400j, (285, 'kpc'):(315, 'kpc'):400j, (285, 'kpc'):(315, 'kpc'):400j)] x_ = np.linspace(-15,15,400) y_ = np.linspace(-15,15,400) z_ = np.linspace(-15,15,400) x,y,z = np.meshgrid(x_,y_,z_, indexing= 'ij')

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[ANN] yt_astro_analysis 1.1 released
by Britton Smith Dec. 15, 2021

Dec. 15, 2021

Greetings! yt_astro_analysis version 1.1 is released! yt_astro_analysis is an extension of yt for astrophysical analysis. This is the first stable release of yt_astro_analysis to be compatible with yt version 4.0 and later. New Features - The HaloCatalog has been significantly refactored (#58 <https://github.com/yt-project/yt_astro_analysis/pull/58>, #62 <https://github.com/yt-project/yt_astro_analysis/pull/62>) with the following additional improvements: - the interface to the Rockstar halo finder is now compatible with the latest version of Rockstar Galaxies #55 <https://github.com/yt-project/yt_astro_analysis/pull/55> - all halo finders now support being run with time-series of datasets - halo particle ids now savable with FoF and HOP halo finders #52 <https://github.com/yt-project/yt_astro_analysis/pull/52> - looping over halos is done with io chunks instead of ds.all_data for a significant speedup and reduction in memory - Allow more flexibility for specifying rockstar particle mass #84 <https://github.com/yt-project/yt_astro_analysis/pull/84> - Add restart option for rockstar #82 <https://github.com/yt-project/yt_astro_analysis/pull/82> - Adding an outer_radius parameter to the iterative COM callback #34 <https://github.com/yt-project/yt_astro_analysis/pull/34> - Remove the sunyaev_zeldovich analysis module. This is now pyxsim <http://hea-www.cfa.harvard.edu/~jzuhone/pyxsim/>. #79 <https://github.com/yt-project/yt_astro_analysis/pull/79> - Drop support for python 3.6 #100 <https://github.com/yt-project/yt_astro_analysis/pull/100>, #101 <https://github.com/yt-project/yt_astro_analysis/pull/101> Minor Enhancements and Bugfixes - significant project management and ci improvements #89 <https://github.com/yt-project/yt_astro_analysis/pull/89>, #90 <https://github.com/yt-project/yt_astro_analysis/pull/90>, #91 <https://github.com/yt-project/yt_astro_analysis/pull/91>, #92 <https://github.com/yt-project/yt_astro_analysis/pull/92>, #96 <https://github.com/yt-project/yt_astro_analysis/pull/96>, #95 <https://github.com/yt-project/yt_astro_analysis/pull/95>, #97 <https://github.com/yt-project/yt_astro_analysis/pull/97>, #108 <https://github.com/yt-project/yt_astro_analysis/pull/108>, #109 <https://github.com/yt-project/yt_astro_analysis/pull/109> - Add annotate_halos function #98 <https://github.com/yt-project/yt_astro_analysis/pull/98> - only access particle_type field in rockstar if it exists and is needed #111 <https://github.com/yt-project/yt_astro_analysis/pull/111> - fix light cone projections with weight fields #37 <https://github.com/yt-project/yt_astro_analysis/pull/37> - Fix HaloCatalog progress bar #40 <https://github.com/yt-project/yt_astro_analysis/pull/40> - clarify rockstar error message about using the wrong number of MPI processes #42 <https://github.com/yt-project/yt_astro_analysis/pull/42>, #113 <https://github.com/yt-project/yt_astro_analysis/pull/113> - check derived_field_list for base fields #43 <https://github.com/yt-project/yt_astro_analysis/pull/43> - allow cosmology splice from a single dataset #49 <https://github.com/yt-project/yt_astro_analysis/pull/49> - Fix iterator #68 <https://github.com/yt-project/yt_astro_analysis/pull/68> - Support new config file format #65 <https://github.com/yt-project/yt_astro_analysis/pull/65> - Enable circleci testing #44 <https://github.com/yt-project/yt_astro_analysis/pull/44> - Add max_box_fraction to plan_cosmology_splice #76 <https://github.com/yt-project/yt_astro_analysis/pull/76> - Fix HaloCatalog output_dir #81 <https://github.com/yt-project/yt_astro_analysis/pull/81> - remove deprecated dm_only keyword from halo finder #57 <https://github.com/yt-project/yt_astro_analysis/pull/57> - update amr_grid.inp #77 <https://github.com/yt-project/yt_astro_analysis/pull/77> New Contributors - Corentin Cadiou (@cphyc <https://github.com/cphyc>) - Nathan Goldbaum (@ngoldbaum <https://github.com/ngoldbaum>) - Meng Yuan Ho (@willsonho2000 <https://github.com/willsonho2000>) - Cameron Hummels (@chummels <https://github.com/chummels>) - Clément Robert (@neutrinoceros <https://github.com/neutrinoceros>) Full Changelog: yt_astro_analysis-1.0.0...yt_astro_analysis-1.1.0 <https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1…> The yt_astro_analysis package lives at: https://github.com/yt-project/yt_astro_analysis Documentation can be found at: https://yt-astro-analysis.readthedocs.io Special thanks to Clément Robert for assembling the machinery to make this release happen! On behalf of the yt-astro development team.

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Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Re: frontend for PLUTO
by Clément Robert Dec. 9, 2021

Dec. 9, 2021

To followup this discussion, I’d like to advertise that I am maintaining a Pluto-friendly external frontend, available on PyPI as well as Github https://pypi.org/project/yt_idefix/https://github.com/neutrinoceros/yt_idef… Starting from version 0.8.0 (released today in response to this discussion), this frontend is intended to explicitly support Pluto VTK files, while previous versions just happened to have partial support. For information, the frontend is currently not in the main yt core base, but will be proposed for inclusion in the future when it’s mature enough. Issues and PRs are welcome there ! Cheers, Clément

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