yt-users February 2021

yt-users@python.org

9 participants
11 discussions

Clump Finding for Gadget2 format
by 201s408s＠stu.kobe-u.ac.jp 21 Feb '22

21 Feb '22

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?

3 8

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

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

8 14

question about spheres
by Stephanie Tonnesen 09 Mar '21

09 Mar '21

Hi yt-users, I have a question about spheres, because I am having a problem that I don't really know how to solve. Basically, I have clusters of stars, and I want to know how many stars are within 6 pc of each star. So, what I have done is taken a sphere at each star position with a radius of 6 pc, and then performed sp.quantities.total_quantity(["particle_mass"]) Now I wanted to double-check this number by brute-force, so I calculated the distance between all the particles and then summed the masses of all the particles that were less than 6 pc. I am not getting the same values--they are close, but not the same (they seem to mostly scatter up or down by a factor of 2). So...to the question!! Because I am measuring particles in a grid code (Enzo) is there any sort of shifting to the grid position instead of using the particle positions here? Because stars are pretty packed I could imagine that this could cause the differences I am seeing. I am not sure that the problem is not something silly I am doing, but wanted to check this possibility as well. Thanks! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

2 5

triage meetings -- early 2021!
by Madicken Munk 03 Mar '21

03 Mar '21

Hi yt-users! It's been a while since we've had scheduled triage meetings during the week. We use triage meetings to do development and maintenance work on the project. If you'd like to help contribute to making yt *better* and maybe even more useful for you, consider attending! All skill levels in development are welcome and encouraged to attend. If you're a bit shy, don't worry, you can also attend and just listen! I've created two polls. The first is morning in central US timezone to hopefully catch times where project members located in Europe can join, and the second is for afternoon/early evening in the central US timezone so project members on the west coast and asia can hopefully join. Vote in whatever poll applies to you (or both if you find all times work). We will choose times to accommodate the most people, and I personally would love to see all of you attend!!! I've put times for next week, but know that these polls are your *general availability *weekly for the next few months. Morning Poll: http://whenisgood.net/tmdfp2i Afternoon Poll: http://whenisgood.net/i2c8n3b - Madicken

1 1

Column Density 1-D Radial Profile
by h.fathie＠gmail.com 27 Feb '21

27 Feb '21

Hello, I would like to plot the HI column density as a function of the radius. To do this I follow these steps. But instead of the column density (in cm-2) the y-axis is number density (in cm-3): fn = '../IsolatedGalaxy/galaxy0030/galaxy0030' ds = yt.load(fn) trident.add_ion_fields(ds, ions = ['H I'], ftype = 'gas') sphere = ds.sphere('c', (100., 'kpc')) plot = yt.ProfilePlot(sphere, 'radius', 'H_p0_number_density', weight_field = None) plot.save('my_fig.png') The field 'H_p0_number_density' should return the column density because it does so when I use the following line of code: plot = yt.ProjectionPlot(ds, 'z', 'H_p0_number_density') plot.save('fig.png') Here the 'H_p0_number_density' is interpreted as column density but not as number density. I would be very grateful if some one could help me with this issue. Many thanks Best regards, Hassan

2 2

yt Help / .SILO Export
by Egeln,Anthony A,Jr 23 Feb '21

23 Feb '21

Good afternoon! I am a PhD student at the University of Florida and am looking to use yt for a relatively specific function. In the past I have used it to create flat grids of data to export and give to other groups. These worked well due to their ability to flatten the adaptive mesh and interpolate between points to provide a nice, smooth mesh. What I would like to do now is be able to iterate through the grids that are stored in the yt object in order to output the whole data array. I need to do this in order to get the full spectrum of data and output it into a different file format (.SILO). The group requesting this information is looking to avoid flattening the data and wants access to the different levels of information in the adaptive mesh. I’ve come across several ways to access information about the individual grids of the stored data. Once I have loaded the file [often as an object called ds, ds = yt.load(file)], I can view information such as the grid names, the number of grids, and the size of grids through functions such as ds.index.grids, etc. Is there another function similar to index that allows the user to call data from an individual grid? For example, with index.grids[XXXX].size I can see that grid XXXX is [16 16 1]. I would like to be able to output that individual grid to an array. If it’s simpler maybe only export the data for say, ‘temperature’. I have found some calls to a similar process in the URL below: https://yt-project.org/doc/quickstart/data_inspection.html Thank you for your time. Please let me know if you are able to provide assistance in this matter. Have a great day! Anthony Egeln Jr. University of Florida anthony.egeln(a)ufl.edu<mailto:anthony.egeln@ufl.edu> 904 652 3159

2 4

No module named 'yt.loaders'
by h.fathie＠gmail.com 23 Feb '21

23 Feb '21

Hello, I have installed yt successfully and then I tried to install 'trident' using the following command pip install trident But when I issued import trident, I got the following error: It seems that it is complaining that loader does not exist in yt. >>> import trident /usr/lib/python3.8/_collections_abc.py:666: MatplotlibDeprecationWarning: The global colormaps dictionary is no longer considered public API. self[key] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/pc/.local/lib/python3.8/site-packages/trident/__init__.py", line 63, in <module> from trident.ray_generator import \ File "/home/pc/.local/lib/python3.8/site-packages/trident/ray_generator.py", line 14, in <module> from trident.light_ray import \ File "/home/pc/.local/lib/python3.8/site-packages/trident/light_ray.py", line 19, in <module> from yt_astro_analysis.cosmological_observation.cosmology_splice import \ File "/home/pc/yt_astro_analysis/yt_astro_analysis/cosmological_observation/cosmology_splice.py", line 19, in <module> from yt.loaders import \ ModuleNotFoundError: No module named 'yt.loaders' >>> I would be grateful if some one could provide some help on this. Best regards, Hassan

2 3

Problem with 'import rockstar_interface'
by h.fathie＠gmail.com 19 Feb '21

19 Feb '21

Dear all, I have installed yt and its associated rockstar but when I execute the following command: from yt.analysis_modules.halo_finding.rockstar import rockstar_interface I get the following error: >>> from yt.analysis_modules.halo_finding.rockstar import rockstar_interface Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/pc/yt-conda/src/yt-git/yt/__init__.py", line 21, in <module> from yt.data_objects.api import ( File "/home/pc/yt-conda/src/yt-git/yt/data_objects/api.py", line 1, in <module> from . import construction_data_containers as __cdc, selection_objects as __sdc File "/home/pc/yt-conda/src/yt-git/yt/data_objects/construction_data_containers.py", line 15, in <module> from yt.data_objects.selection_objects.data_selection_objects import ( File "/home/pc/yt-conda/src/yt-git/yt/data_objects/selection_objects/__init__.py", line 1, in <module> from .boolean_operations import ( File "/home/pc/yt-conda/src/yt-git/yt/data_objects/selection_objects/boolean_operations.py", line 5, in <module> from yt.data_objects.selection_objects.data_selection_objects import ( File "/home/pc/yt-conda/src/yt-git/yt/data_objects/selection_objects/data_selection_objects.py", line 11, in <module> from yt.data_objects.data_containers import YTDataContainer File "/home/pc/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 8, in <module> from yt.data_objects.profiles import create_profile File "/home/pc/yt-conda/src/yt-git/yt/data_objects/profiles.py", line 14, in <module> from yt.utilities.lib.misc_utilities import ( File "yt/utilities/lib/misc_utilities.pyx", line 1, in init yt.utilities.lib.misc_utilities ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject >>> I would be grateful if some one could help me with this issue. With best regards, Hassan

2 1

Toomre's criterion
by Cynthia Saad 15 Feb '21

15 Feb '21

Dear all, Did anyone calculate and plot the toomre criterion of a disk from an enzo dataset? Any tips on how to do that? Best, Cynthia

2 1

Relaunch of the yt-project blog!
by Madicken Munk 03 Feb '21

03 Feb '21

Hi yters! I have been working of a relaunch of the yt blog with Matt over the past few weeks (it was previewed at the RHytHM workshop if you want to watch the talk about it (linked below)! Check it out at https://blog.yt-project.org/ Some of the things we tried to do when relaunching the blog was: - find a format that allowed for easy filtering of posts (in this blog we have tags, categories, and a search feature) - Find a format that has a nice post preview (with images) - Choose something that is accessible to various levels of contribution. We would love your feedback and contributions on the new blog! What can make it *even better*? What topics would you like to see on the blog? What could *you* add to the blog???? I personally think it would be cool to see stuff like: - How you use yt for YOUR SCIENCE - What cool tips and tricks do you use in yt? - Do you have a favorite feature? What is it and why? - Did you write a cool extension that uses yt? Let's hear about it! - Do you have a very cool colormap theme that you use with yt based on album covers of an artist??? What does science data look like with them??? - And so much more! We have two different ways of contributing a blog post: either as an issue or as a PR. You can check out the differences in the contributor guide. We've moved the blog repo into the yt project organization, it is now located at https://github.com/yt-project/blog You can find the blog hosted at https://blog.yt-project.org/ I can't wait to see all of your posts!!! Madicken PS -- Chris Havlin has already contributed two new posts to the blog! Dask! Napari! So many cool things! Check them out.

1 1

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users February 2021