Mailman 3 January 2022 - 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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[ANN] yt_astro_analysis 1.1.1 released
by Britton Smith Jan. 27, 2022

Jan. 27, 2022

Greetings, I'm pleased to announce the release of yt_astro_analysis version 1.1.1. yt_astro_analysis is a yt extension package for astrophysical analysis. This package contains functionality for: - Halo finding and analysis - Lightcones - Planning cosmological simulations for making lightcones and lightrays - Exporting to the RADMC-3D radiation transport code - Creating PPV FITS cubes This is a bugfix release; no new features have been added. Bugfixes - Make sure to initialize index before checking particle types #127 <https://github.com/yt-project/yt_astro_analysis/pull/127> - Fix broken example with halo plotting #132 <https://github.com/yt-project/yt_astro_analysis/pull/132> - Make total particles a 64 bit integer #133 <https://github.com/yt-project/yt_astro_analysis/pull/133> - Set output directory properly for rockstar halo finder #134 <https://github.com/yt-project/yt_astro_analysis/pull/134> Full Changelog: yt_astro_analysis-1.1.0...yt_astro_analysis-1.1.1 <https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1…> Enjoy! - team yt-astro

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office hours this Friday
by Matthew Turk Jan. 27, 2022

Jan. 27, 2022

Hi all, On Friday I'll be holding "yt office hours" at 9:30AM Central (10:30AM Eastern, 3:30PM GMT). I'll announce the URL on Slack in #general just beforehand, but the stream will *probably* be at twitch.tv/powersoffour . If you have questions about yt, or want to get your feet wet developing or see how code review and whatnot happens, please stop on by! -Matt

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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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Question about YT Filter Part
by 贺一峰 Jan. 26, 2022

Jan. 26, 2022

Hi, everyone! I met trouble when I used YT-fliter part. At first, I have tried exclude_ function, however, it said that there is no such an attribute. The version of my YT is 3.5.0, I donnot know if it is because of the old version. Here is the error info: ------------------------------------------------------------------------------------------------------------------------------- File "vorfield.py", line 85, in <module> vort_ds=ds.exclude_inside(('boxlib','vort_z'),-1e3,1e3) P000 yt : [ERROR ] 2022-01-26 17:34:53,155 AttributeError: 'BoxlibDataset' object has no attribute 'exclude_inside' application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 -------------------------------------------------------------------------------------------------------------------------------- Then I tried cut_region function, however, it said that some argument is lost and I donnot know why. Here is the error info: --------------------------------------------------------------------------------------------------------------------------------------------- File "vorfield.py", line 82, in <module> vort_ds = ds.cut_region(['(obj["boxlib", "vort_z"] > 1e3)']) P000 yt : [ERROR ] 2022-01-26 17:07:37,086 TypeError: __init__() missing 1 required positional argument: 'conditionals' application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 ---------------------------------------------------------------------------------------------------------------------------------------------- I will be appreciate if anybody can help me! Thank all! He Yifeng

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import SWIFT snapshot into yt
by Romeel Davé Jan. 26, 2022

Jan. 26, 2022

Hi, Has anyone tried to import a snapshot from SWIFT (https://swift.dur.ac.uk/) into yt? yt.load(SNAPSHOT) gives me the traceback: >>> yt.load('eagle_0149.hdf5') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/loaders.py", line 93, in load return candidates[0](fn, *args, **kwargs) File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/frontends/swift/data_structures.py", line 41, in __init__ default_species_fields=default_species_fields, File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/frontends/sph/data_structures.py", line 43, in __init__ default_species_fields=default_species_fields, File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 1934, in __init__ default_species_fields=default_species_fields, File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 228, in __init__ self._parse_parameter_file() File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/frontends/swift/data_structures.py", line 103, in _parse_parameter_file runtime_parameters = self._get_info_attributes("RuntimePars") File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/yt/frontends/swift/data_structures.py", line 84, in _get_info_attributes header = dict(handle[dataset].attrs) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/cosma/home/dc-dave2/anaconda3/lib/python3.7/site-packages/h5py/_hl/group.py", line 264, in __getitem__ oid = h5o.open(self.id, self._e(name), lapl=self._lapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5o.pyx", line 190, in h5py.h5o.open KeyError: "Unable to open object (object 'RuntimePars' doesn't exist)" >>> The snapshot format is similar to Gadget but it appears RunTimePars are in other fields. Here are the hdf5 fields: $ h5ls eagle_0149.hdf5 BHParticles Soft Link {/PartType5} Cells Group Code Group Cosmology Group DMParticles Soft Link {/PartType1} GasParticles Soft Link {/PartType0} GravityScheme Group Header Group HydroScheme Group InternalCodeUnits Group Parameters Group PartType0 Group PartType1 Group PartType4 Group PartType5 Group PhysicalConstants Group Policy Group StarsParticles Soft Link {/PartType4} StarsScheme Group SubgridScheme Group Units Group UnusedParameters Group Some of the other field names within PartType0 etc are also somewhat different, e.g. MetalMassFractions instead of Metallicity. thanks, romeel

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Question about Filter Part
by hyf＠stu.pku.edu.cn Jan. 26, 2022

Jan. 26, 2022

Hi, everyone! I met trouble when I used YT-fliter function At first, I have tried exclude_ function, however, it said that there is no such an attribute. The version of my YT is 3.5.0, I donnot know if it is because of the old version. Here is the error info: ------------------------------------------------------------------------------------------------------------------------------- File "vorfield.py", line 85, in <module> vort_ds=ds.exclude_inside(('boxlib','vort_z'),-1e3,1e3) P000 yt : [ERROR ] 2022-01-26 17:34:53,155 AttributeError: 'BoxlibDataset' object has no attribute 'exclude_inside' application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 -------------------------------------------------------------------------------------------------------------------------------- Then I tried cut_region function, however, it said that some argument is lost and I donnot know why. Here is the error info: --------------------------------------------------------------------------------------------------------------------------------------------- File "vorfield.py", line 82, in <module> vort_ds = ds.cut_region(['(obj["boxlib", "vort_z"] > 1e3)']) P000 yt : [ERROR ] 2022-01-26 17:07:37,086 TypeError: __init__() missing 1 required positional argument: 'conditionals' application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 ---------------------------------------------------------------------------------------------------------------------------------------------- I will be appreciate if anybody can help me! Thank all! He Yifeng

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Plotting particles efficiently for a cosmological simulation
by dongpaez＠iap.fr Jan. 19, 2022

Jan. 19, 2022

Hi all, I am trying to plot the spatial distribution of stars and DM for a large simulation. For my simulation, yt.ProjectionPlot (using deposited fields) is very slow, so it is not very convenient given that I need to produce a large amount of plots. I have also tried yt.ParticlePlot, which is much faster but the default grid size is too small, and so for low particle densities it is very difficult to see individual particles. I haven't found the way to increase the grid size, since x_bins and y_bins can't seem to be modified for a ParticleProjectionPlot (only for ParticlePhasePlot). I have also considered using annotate_particles, but it doesn't give as much information about the density of particles integrated over the line of sight. Reducing alpha doesn't solve the problem. Is there any better way to approach this? Thanks in advance!!

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