Mailman 3 - yt-users

Ramses boundary particles
by Thor Tepper-Garcia 07 Oct '24

07 Oct '24

Hi, As other Ramses user probably know, sometimes particles can end up at the box boundaries, which effectively means they have left the simulation volume. I've noticed however that when reading in a Ramses snapshot, YT tends to keep the particles at the lower end of the boundaries (e.g. x =< 0 in c.u.), but removes all beyond the upper end (e.g. x >= 1. in c.u.). This may significantly bias the centre of mass when calculated using particles. Thus my question is: How do I tell YT to either ignore or include all boundary particles when loading a snapshot? Cheers Thor.

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"ValueError: Unable to avoid copy" when attempting to plot
by nmarshak＠sci.utah.edu 14 Aug '24

14 Aug '24

Greetings, yt is failing when I attempt to plot Nyx data with "ValueError: Unable to avoid copy while creating an array as requested." Input data: http://use.yt/upload/79bb1749 Script: https://paste.yt-project.org/show/644/ Output: https://paste.yt-project.org/show/645/ Is this a bug? Am I doing something wrong here? Sincerely, Nathan

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Multipanel with PhasePlot
by HyeonYong Kim 14 Aug '24

14 Aug '24

Dear YT user, I'm trying to draw a multipanel Phaseplot in yt. There is no problem with drawing the plot, but the problem is the size of figure. As shown in my figure (https://drive.google.com/file/d/1IM_slIts1lgtQ95m-sKHf7EncIM2ZvoO/view?usp=…) or yt document here (https://yt-project.org/doc/cookbook/complex_plots.html#multipanel-with-phas…), the images are compressed, not the square shape. I tried fig = plt.figure(figsize = (2,8)) but it doesn't work and the set_figure_size function is only for the size of the figure on the longest axis. I've searched the YT document, it seems that there is no function that adjusts the width or height of the figure. Each image comes out as a square if I draw the multipanel with Projectionplot, it doesn't work with Phaseplot. Is there any way to handle the size of the figures or axesgrid in YT? Thanks in advance. Hyeonyong

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problem with quickstart notebook
by eleonora.panini7jkd＠gmail.com 13 Aug '24

13 Aug '24

I can't visualize the quickstart notebook tutorial: https://yt-project.org/doc/quickstart/index.html When I click the links: 'introduction' , 'data inspection' and so on.. I blank page appears, without visualizing any text. How can I try the tutorial? It seems also that if I install yt and git che quickstart tutorial, when I go into the respective folder is empty.

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YT and FLASH2.5
by Jordi 02 Aug '24

02 Aug '24

Hello yt-users! I am using yt to analyze simulations performed with the latest version of FLASH4.7, and everything works fine. However, I am not able to load some old files performed with FLASH2.5. Do these old files require specific commands? Is FLASH2.5 incompatible with the newest version of yt? Thank you! Jordi

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Rays
by Daniel 12 Jun '24

12 Jun '24

Hello my name is Daniel, I have been working with yt for a couple months and it has been really useful. I have found the ray method very useful but I have been wondering if there was a possibility to be able to print out a ray like an array. What I mean is if there is a way to use a ray to grab information along that ray and be able to iterate through it like an array to be able to print it out into a file or just print in general. If this is not possible is there any other method I should use to be able to get a line of information between two points and be able to print it out somewhere? Also if possible I would also like it to be able to annotate it on a graph like a ray so I can see where exactly I'm grabbing but if not that is fine. Thank you, Daniel

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Some problems with the yt-project about the cosmological simulations
by Shiwu Zhang 03 Jun '24

03 Jun '24

Dear yt-project users, I am a postdoc studying the high redshift galaxy at Tsinghua University, China. Recently, I am trying to project the output of the FIRE cosmological simulations to a mesh grid in the structure of the RAMSES octree with the yt-project. I attempt to use `yt.geometry.oct_container.RAMSESOctreeContainer` to do this job. Since the tutorial of the yt-project is short, Could you please give me an example script on how to do this work? FIRE simulations are run with the gizmo code (SPH), it provides me with a list of gas particles with the position, density, temperature, and etc. Any response would be more than appreciated! Thank you very much! Best regards, Shiwu ------------------------------------------ Shiwu Zhang Postdoc Tsinghua University zsw18(a)tsinghua.org.cn Telephone: +86-18801095798

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Upcoming UIUC summer school on research software + open science
by Madicken Munk 30 May '24

30 May '24

Hi yt-users, Are you a researcher based in the US that has been considering how software impacts your research? Do you already use research software or develop scripts in your day-to-day work? Do you want to make your scientific workflow open and accessible to people in and outside of your research group? If this sounds like you, then you may be interested in an upcoming URSSI ( https://urssi.us/) summer school that I'm helping to organize that brings together concepts of open science and research software engineering. *Applications are open through June 06! *Travel support and attendance costs are covered by the school. https://urssi.us/blog/2024/05/20/applications-now-open-for-a-summer-school-… Ideal candidates are people who have a Carpentries workshop-level knowledge of the shell, git, and python and want to learn principles of open science and research software engineering for their research. We'll be building off of these foundational skills in this school. Participants from all research disciplines (the sciences, humanities, engineering, social science, economics, etc.) that use software are welcome! If you’re interested, please consider applying! If you have any questions about the school, I am happy to answer them at mmunk2(a)illinois.edu . Madicken Munk

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How to get the np.array of profile plots
by hyf＠stu.pku.edu.cn 30 May '24

30 May '24

Hi, all, I am trying to use matlibplot to plot the profile of a sphere object, so I need to get the np.array of profile plots. I know that we can use "slc.frb" to get the np.array of SlicePlot. However, I don't find the simliar function in profile plots, how can I get the np.array of a sphere object's profile? Thanks a lot for every suggestion or help. best wishes, Yifeng He

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ANN: Grackle 3.3 released!
by Matthew Abruzzo 28 May '24

28 May '24

Grackle 3.3 is released! Grackle is a chemistry and radiative cooling solver for astrophysical simulations and models. The Grackle 3.3 release consists of 20 pull requests from 5 contributors, 2 of them new to the project. It contains 1 new feature, 2 minor enhancements, 5 bugfixes, and some documentation improvements. 8 previously deprecated functions have also been removed. See below for further details. This also marks the release of version 1.0.1 of Pygrackle (the Python interface to Grackle). *New Features* * Add temperature floor field #159 <https://github.com/grackle-project/grackle/pull/159> *Minor Enhancements* * Refactor the `cloudy_data` struct so that the `grid_{dimension,parameters}` members are fixed-size arrays #167 <https://github.com/grackle-project/grackle/pull/167> * Add error-check on `grackle_field_data.grid_dx` #190 <https://github.com/grackle-project/grackle/pull/190>, #191 <https://github.com/grackle-project/grackle/pull/191> *Bugfixes* * Minor tweaks to `initialize_rates.c` #168 <https://github.com/grackle-project/grackle/pull/168> * explicitly initialize all struct members to solve plethora of issues #166 <https://github.com/grackle-project/grackle/pull/166> * Fix memory leak #169 <https://github.com/grackle-project/grackle/pull/169> * Add missing fields to pygrackle #173 <https://github.com/grackle-project/grackle/pull/173> * Fix pygrackle H number density and mean molecular weight calculations in #180 <https://github.com/grackle-project/grackle/pull/180> *Documentation Updates* * Add mention of c_local_example to docs #174 <https://github.com/grackle-project/grackle/pull/174> * Fix a minor typo in documentation related to `grid_dx` #176 <https://github.com/grackle-project/grackle/pull/176> * Document release procedure and describe versioning policy #194 <https://github.com/grackle-project/grackle/pull/194> *Infrastructure Updates* * Introduce `c_local_example` and fixed inconsistencies in `c_example` #170 <https://github.com/grackle-project/grackle/pull/170> * Update linux-gnu makefile #183 <https://github.com/grackle-project/grackle/pull/183> * Add `c_local_example` to list of executable removed by `make clean` #186 <https://github.com/grackle-project/grackle/pull/186> * Factor out some file-generation machinery #181 <https://github.com/grackle-project/grackle/pull/181> *Removed Functions* All functions deprecated in the 3.2 release were fully removed in #184 <https://github.com/grackle-project/grackle/pull/184>. The functions include: * `_solve_chemistry`, `_calculate_cooling_time`, `_calculate_gamma`, `_calculate_pressure`, `_calculate_temperature` * `_set_default_chemistry_parameters`, `_initialize_chemistry_data`, `_free_chemistry_data` *Contributors* * Britton Smith (@brittonsmith <https://github.com/brittonsmith>) * Ewan Jones (@EwanBJones98 <https://github.com/EwanBJones98>) * Matthew Abruzzo (@mabruzzo <https://github.com/mabruzzo>) * Mladen Ivkovic (@mladenivkovic <https://github.com/mladenivkovic>) (new!) * @tiapac <https://github.com/tiapac> (new!) *Grackle Advisory Council* * Matthew Abruzzo * Greg Bryan * Desika Narayanan * Marta Reina-Campos * Britton Smith * Matthew Turk *Full Changelog:* https://github.com/grackle-project/grackle/compare/grackle-3.2.1...grackle-…

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