Mailman 3 November 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. 14, 2022

Aug. 14, 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. 26, 2022

Jan. 26, 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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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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frontend for PLUTO
by Shaokun Xie Dec. 8, 2021

Dec. 8, 2021

Hi all, I'm working with PLUTO now and require some analysis tools which are provided by yt, such as OffAxisProjection. However, I found PLUTO data is only supported in Chombo HDF5 format so far. I have some initial setups which are conflict with chombo library. So does anyone know how to analyze general format data of PLUTO, such as .dbl and .vtk, with yt? btw, I'm also wondering how complex it is if I want to create a frontend for the general format data of PLUTO. Is that all stuff mentioned in https://yt-project.org/doc/developing/creating_frontend.html? Shaokun Xie

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FLASH particle data io - missing data
by Slavin, Jonathan Nov. 11, 2021

Nov. 11, 2021

Hi all, I'm doing calculations that include particles with FLASH and reading in the data with yt. I've had an issue with losing particles, or so I thought. However I noticed that particles with tags that I thought were lost are present at later times. Then, looking at the data with hdfview, I see that it seems that the data is there in the tracer particles array, but yt doesn't return the last row of the table. It works when none of the particles are lost (i.e. have blk = -1), but when there are particles like that it seems that it also loses another particle, whichever happens to be last in the array. The behavior could be more complicated than that, but that's what I've seen so far. I've looked at the code in frontends/flash/io.py but don't see anything obvious that could cause that. Any help would be appreciated. Regards, Jon -- Jonathan D. Slavin Astrophysicist - High Energy Astrophysics Division Center for Astrophysics | Harvard & Smithsonian Office: (617) 496-7981 | Cell: (781) 363-0035 60 Garden Street | MS 83 | Cambridge, MA 02138

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Fwd: Astronomical software development workshop, May 16–20, 2022, @ CCA
by Stephanie Tonnesen Nov. 10, 2021

Nov. 10, 2021

Hi yt community! I just heard about this meeting being held this upcoming May 2022 at the CCA about open source development practices. I think many of us might be interested! If so you can sign up to get updates about the meeting. Best, Stephanie Dear colleagues, We are planning a workshop focused on topics in open source software development practices for astronomy, held in person at the Center for Computational Astrophysics in New York City, May 16–20, 2022. The program and scope are still in development, but we expect it to be of interest to astronomers with a wide range of open source experience, and across all career stages. The schedule will include a large fraction of unstructured time for participant-driven discussion, collaboration, and co-working. For more information about this workshop and to sign up to hear more details as they become available, please check out our website at https://code.astrodata.nyc Please share this email with your department lists and/or anyone else who you think might be interested in participating in this event. Best, Dan (on behalf of the organizing committee) -- Dan Foreman-Mackey Associate Research Scientist, Flatiron Institute http://dfm.io

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Yt colormaps are moving to their own repo
by Clément Robert Nov. 1, 2021

Nov. 1, 2021

Hello yt-folks ! yt native colormaps now have their own package, already available on PyPI https://pypi.org/project/cmyt/ This has two important implications: 1) This message is addressed to anyone who installed yt from source and updates their install regularly. If that’s not your case you can jump to the second item So I’m reaching out to raise awareness about an upcoming change to yt's main branch https://github.com/yt-project/yt/pull/3441 In short: You need to install it to keep your local install working after the PR above is merged You can perform the installation right now if you wish to, you don’t need to wait on the PR to get merged. Run python -m pip install cmyt And you’re done ! Conda-distribution is planned to land soon after the pull request is merged. 2) you can now use yt’s colormaps with raw matplotlib and outside of yt if you want to. See cmyt’s documentation (one page). Cheers ! Clément

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