Mailman 3 April 2022 - 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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Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

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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Setting parameters in the derived fields
by We-An Chen 28 Apr '22

28 Apr '22

Hi all, I'm new to this forum to find some help when setting a new derived field. The situation is that I want to obtain the plane-of-sky components of a vector field (e.g. magnetic field), so I follow (https://yt-project.org/doc/developing/creating_derived_fields.html#a-more-c…) and try something like this for testing my code: def _project_B(field, data): vector = data.get_field_parameter("vector") Bobs = data["gas", "magnetic_field_x"]*vector[0]+data["gas", "magnetic_field_y"]*vector[1]+data["gas", "magnetic_field_z"]*vector[2] return Bobs yt.add_field( ("gas", "project_B"), function=_project_B, sampling_type="cell", units="G", take_log=False, validators=[ValidateParameter(["vector"])], ) npix = 256j ds = yt.load('output_00017/info_00017.txt') sp = ds.r[::npix, ::npix, ::npix] sp.set_field_parameter("vector", yt.YTArray([0., 1., 0.], "dimensionless")) # it can be x/y vector when using off-axis projection Bproj = sp['gas', 'project_B'].value , which returned yt.utilities.exceptions.YTFieldNotFound: Could not find field ('gas', 'project_B') in info_00017 However, if I set "vector" -> "bulk_velocity", it works! Is there something I understand wrong? Best, Wei-An

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JOB: yt development at University of Illinois
by Matthew Turk 21 Apr '22

21 Apr '22

Hi folks! https://jobs.illinois.edu/academic-job-board/job-details?jobID=162846 I'm writing to share with you a job posting to work at the University of Illinois in the School of Information Sciences developing yt and working on community-centric issues. In practice, this would mean working on things related to getting yt and dask to play more nicely together (which Chris Havlin is also working on), working on bridging yt with other domains of study beyond astronomy, trying to make yt easier (and more fun) to use, and helping to grow the yt community. You would be welcomed to Champaign-Urbana, but this position can also be remote. This posting is very similar in spirit to one I shared in 2020 -- the position may be particularly interesting to individuals looking to transition to industry, as well as those who are interested in pursuing jobs in academia that are more focused on research software. This job is posted as part of the School of Information Sciences, but it's within a research group that spans the National Center for Supercomputing Applications (NCSA), the Astronomy department, the Institute for Genomic Biology, Materials Sciences, and other groups and institutes on campus. This position will also provide ample opportunities for interdisciplinary work with academics, the open source scientific software ecosystem (SciPy, PyData, etc) and for travel and professional development. You'd get to work with folks involved in yt and you'd get to have a hand in developing and designing some really fun tools for data analysis and visualization. Please do reach out to let me know if you have any questions about the opportunity, and if you know anyone you think might be interested, it would be very helpful if you could pass this information along to them. Thanks, Matt

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trouble reading HDF5
by tylee＠khu.ac.kr 18 Apr '22

18 Apr '22

My hdf5 file looks something like this Header ... PartType0 Coordinates ... ElementAbundance Hydrogen Helium ... Mass .... PartType4 ... I know how to read some data ds = yt.load(fname) ad = ds.all_data() print(ad[('PartType0', 'Mass')]) .... but I don't know how to read the data such as Hydrogen in ElementAbundance in PartType0 How can I do that?

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yt 4.0.3 is released !
by Clément Robert 17 Apr '22

17 Apr '22

Announcing yt 4.0.3 ! This is a bugfix release, all users are recommended to upgrade. It includes a critical bugfix for particle data analysis, as well as a ~20 bug fixes, most notably for 2D plotting and loading RAMSES data. It is available on PyPI as well as conda-forge. See the Github release notes for more: https://github.com/yt-project/yt/releases/tag/yt-4.0.3 Clément for the yt dev team

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Issue with changing from code units to real units on Gadget-2 files
by moonpigeona＠gmail.com 17 Apr '22

17 Apr '22

I've been attempting to look at a Gadget-2 file's temperature by converting the code units into real units, by using the unit_base argument but I haven't been able to alter the temperature in any way. I am wondering if anyone knows how to convert the gadget units of temperature? The temperature for my simulation is not individually given to each particle but is derived from the internal energy and chemical abundance. Any help would be greatly appreciated. These are my imports import yt import soxs import pyxsim import numpy as np This is the code fname = '/Users/Andrew/Downloads/output_00056/new_180' unit_base = {'UnitLength_in_cm' : 1.2e+17, 'UnitTime_in_yr' : 61.03633, 'UnitVelocity_in_cm_per_s' : 6.23e+7, 'UnitMass_in_g' : 6.97e+39, 'UnitTemp_in_K' : 3.568e+7} bbox_lim = 850 #kpc bbox = [[-bbox_lim,bbox_lim], [-bbox_lim,bbox_lim], [-bbox_lim,bbox_lim]] ds = yt.load(fname,unit_base=unit_base,bounding_box=bbox,default_species_fields="ionized") ds.index ad= ds.all_data() This is the ds field list: ('Bndry', 'Coordinates'), ('Bndry', 'Mass'), ('Bndry', 'ParticleIDs'), ('Bndry', 'Velocities'), ('Gas', 'Coordinates'), ('Gas', 'Density'), ('Gas', 'InternalEnergy'), ('Gas', 'Mass'), ('Gas', 'ParticleIDs'), ('Gas', 'SmoothingLength'), ('Gas', 'Velocities'), ('Halo', 'Coordinates'), ('Halo', 'Mass'), ('Halo', 'ParticleIDs'), ('Halo', 'Velocities'), ('Stars', 'Coordinates'), ('Stars', 'Mass'), ('Stars', 'ParticleIDs'), ('Stars', 'Velocities'), ('all', 'Coordinates'), ('all', 'Mass'), ('all', 'ParticleIDs'), ('all', 'Velocities'), ('nbody', 'Coordinates'), ('nbody', 'Mass'), ('nbody', 'ParticleIDs'), ('nbody', 'Velocities')]

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How to change values of yt fields
by Nina Akerman 08 Apr '22

08 Apr '22

Hi everyone, The problem: I create a derived field filled with zeros: def _accel_x(field, data): return data['relative_x'] * 0.0 / yt.units.s**2 ds.add_field(('gas', 'accel_x'), units='cm/s**2', function=_accel_x, sampling_type='cell’) I then fetch all data and check that ‘accel_x’ field is indeed zeros: ad = ds.all_data() ad['accel_x’] YTArray([-0., -0., -0., ..., 0., 0., 0.]) cm/s**2 I figured I could set the values in a derived field in the following way: ad['accel_x'] = a_gas[:, 0] ad['accel_x'] = a_gas[:, 1] ad['accel_x'] = a_gas[:, 2] where a_gas is a numpy array of shape (number of cells in ad, 3). I need it because I don’t think there is a way to do define a_gas directly in a derived field. Indeed, now ‘accel_x’ is not zeros ad['accel_x’] YTArray([ 1.41986331e-11, 1.46817279e-11, 1.50849113e-11, ..., -3.98769430e-11, -4.35244006e-11, -4.74626863e-11]) cm/s**2 Unfortunately, when I need to use PhasePlot or ProjectionPlot or create_profile, the results I’m getting are such as if ‘accel_x’ was still zeros. So is there a correct, definitive way to change the values of a derived field? Thank you, Nina

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YTUnidentifiedDataType: Could not determine input format
by yurinakazato0207＠g.ecc.u-tokyo.ac.jp 08 Apr '22

08 Apr '22

Hi, I try to make a projection figure by yt. My output data is from ART simulation. I tried the following command , ds = yt.load("../FirstLight/test/FL633_G016.a0.115.dat") but there is an error. YTUnidentifiedDataType: Could not determine input format from `'../FirstLight/test/FL633_G016.a0.115.dat'`. I googled this error and tried ds = yt.load_amr_grids() but still doesn't work. Are there any solutions?

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