yt-users September 2018

yt-users@python.org

11 participants
15 discussions

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

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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How to make the new drived-fields work?
by lianxiaoli87＠sjtu.edu.cn 10 Oct '18

10 Oct '18

Hi, I have written some new fields in yt/yt/fileds file named as XXX.py, but I have no idea how to make it work correctly like kinetic-energy, thermal-energy etc which can be projected and sliced. Please help me to work it out!!!

2 4

clump finder error with maximum density set
by Stephanie Tonnesen 04 Oct '18

04 Oct '18

Hi yt-users! I have been fiddling some more with yt's clump finder and have another question. I want to use density to find clumps, but want my maximum threshold value to be below the fiducial setting--instead of above the maximum possible density in the code I just want the finder to stop searching at, say 3.2e-24. The code was working but running out of memory until I set the max threshold, and I now get this error: ....lots of pleasant looking output messages.... Updating joins ... : 0%| | 0/7 [00:00<?, ?it/s] Updating joins ... : 100%|██████████| 7/7 [00:00<00:00, 48933.55it/s] yt : [INFO ] 2018-09-07 14:08:55,007 Investigating 2 children. yt : [INFO ] 2018-09-07 14:08:55,007 Finding clumps: min: 3.200000e-24, max: 3.200000e-24, step: 2.000000 yt : [INFO ] 2018-09-07 14:08:55,041 Finding clumps: min: 3.200000e-24, max: 3.200000e-24, step: 2.000000 yt : [INFO ] 2018-09-07 14:08:55,042 Eliminating invalid, childless clump with 2 cells. yt : [INFO ] 2018-09-07 14:08:55,042 1 of 2 children survived, linking its children to parent. Traceback (most recent call last): File "yt_clump_fingert.py", line 59, in <module> find_clumps(master_clump, c_min, c_max, step) File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", line 444, in find_clumps find_clumps(child, min_val*d_clump, max_val, d_clump) File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", line 438, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", line 438, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", line 438, in find_clumps find_clumps(clump, min_val*d_clump, max_val, d_clump) File "/mnt/home/stonnesen/yt-conda/yt/yt/analysis_modules/level_sets/clump_handling.py", line 461, in find_clumps for child in clump.children: TypeError: 'NoneType' object is not iterable I tried to circumvent this error by changing my max to 2e-24 (not a multiple of 2 of 1e-25), and got the same error when the min was 3.2e-24 and the max was 2e-24 (!). Is there any way I can get around this error and have the clumpfinder stop looking once it has clump edges at my maximum density? Thanks! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

4 13

NumFOCUS new contributor recognition
by Nathan Goldbaum 27 Sep '18

27 Sep '18

Hello all, I’d like to extend my congratulations to Ashley Kelly and Corentin Cadiou for winning the innaugural NumFOCUS new contributor award! https://numfocus.org/blog/inaugural-numfocus-awards-and-new-contributor-rec… This is a new award that honors new contributors to NumFOCUS projects. The yt executive committee nominated Ashley and Corentin and they were both recognized at the awards dinner on Sunday night after the sustainability summit. Let’s all give a warm round of emoji applause! 👏👏👏👏👏👏👏👏 Nathan Ashley Kelly Ashley Kelly participated in Google Summer of Code this year with yt via the NumFOCUS umbrella org. rom the outset, Ashley proposed a very ambitious plan. Privately I felt that the plan was probably overambitious but with the expectation that we would likely descope the plan, we decided to press ahead wit the project. Not only did we not need to descope, In my opinion Ashley exceeded his original plans. We are now in a much better position to ship major new features next year thanks to Ashley’s efforts. Corentin Cadiou Corentin Cadiou began contributing to yt completely unprompted by any of the core developers, working from Europe without in-person contact from the bulk of the yt contributor base in the United States. Corentin has substantially improved support for simulation data produced by the RAMSES code, and has contributed a number of other bugfixes, performance improvements, and nice new features. Corentin has doggedly made sure that his code gets merged and regularly helps out new users on Slack and the mailing list. Thanks to his efforts future RAMSES users and users of octree AMR codes will have a much nicer experience with yt than when he began contributing.

2 1

New installation, yt loading error
by Paco Holguin 23 Sep '18

23 Sep '18

Hi, I recently tried to re-install yt on my home directory of a local cluster. I used the all in one script. After installation I added the yt path to the PATH environment variable. The installation looks ok, and the command "yt --help" works. However, when I try to load data, which worked with a previous installation, I get this error: Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import yt >>> yt.load("disk_mhdhdf5_chk_0020") python: /home/conda/feedstock_root/build_artifacts/libnetcdf_1535659474245/work/libsrc4/nc4var.c:431: nc4_vararray_add: Assertion `var->varid == grp->vars.nelems' failed. Aborted (core dumped) Does anyone know what this means? I must have missed something in the setup. I haven't used conda before. Thanks! Paco

2 3

Need help testing the new nightly builds
by Bili Dong - Gmail 17 Sep '18

17 Sep '18

Dear yt users, We are currently testing the revived nightly builds of yt. It would be enormously helpful to have some real-world testing before making it official. And we need your help! We have set up the system so that the latest development version of yt could be installed from our custom anaconda channel using the command: >>> conda install -c yt-project/label/dev yt If you have a few minutes time, you could help testing doing the following: 1. Install yt using the command above in a fresh conda environment. 2. Try some simple yt scripts, like loading a dataset. 3. Report back here whether it is a success and whatever issues you have encountered. Also include the system information (Linux, macOS, Windows) and Python version (2.7, 3.5, 3.6, 3.7). For people more developer-minded, we welcome your comments in the pull request: yt-project/yt#2030 <https://github.com/yt-project/yt/pull/2030>. Thanks in advance for your invaluable feedback! Best regards, Bili

1 0

Rockstar help
by Cynthia Saad (Student) 17 Sep '18

17 Sep '18

hi all i am trying to install rockstar, but make gives a lot of warning then it does work. this is the outcome of make lib in rockstar directory https://justpaste.it/7d4x7 your input is highly appreciated! thanks cynthia Cynthia Saad

2 1

How to make the new drived-fields work?
by lianxiaoli87＠sjtu.edu.cn 17 Sep '18

17 Sep '18

Hi, I write some new fields in yt/yt/fields named as XXX.py, but I have no idea about how to make it work correctly like yt's density, temperature etc which can be projected or sliced plots.

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yt-users September 2018