yt-users July 2016

yt-users@python.org

22 participants
23 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.

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Problem when run yt dev in parallel on Blue Waters
by Pengfei Chen 23 Aug '16

23 Aug '16

Hi all, I have trouble running yt in parallel on Blue Waters. I installed yt using miniconda, the version of yt is ~/miniconda/lib $yt version yt module located at: /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg The current version and changeset for the code is: --- Version = 3.3-dev Changeset = 90f900be7a36+ yt Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried to make the following simple output in parallel, I get: import yt yt.enable_parallelism() from yt.utilities.parallel_tools.parallel_analysis_interface import\ parallel_objects, communication_system comm = communication_system.communicators[-1] print comm.rank, comm.size 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 ... When I run a similar code but with yt-2.x also on Blue Waters, I get what I expect: 7 16 15 16 6 16 9 16 11 16 8 16 0 16 4 16 ... I'm confused about it. Could anyone give me some suggestions please? Thanks, Pengfei

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Slice plot in FITS format
by Prateek Gupta 01 Aug '16

01 Aug '16

Dear Yt users I want to save the slice plot in FITS or HDF5 format. How can I do this in yt once I plot the slice plot of derived field. Many thanks in advance Regards Prateek

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Downsampling AMR data for plotting isocontours
by Daniel Fenn 28 Jul '16

28 Jul '16

Hi, I'm trying to figure out the best way to downsample FLASH AMR data for making isocontours. I'd like to be able to specify the maximum refinement level that should be used for creating the isocontours. My first thought was to use a covering grid, but I'm uncertain how to use that to create a YTSurface object. If anyone can offer any suggestions, I'd appreciate it. Thanks, Dan

2 2

loading Gadget outputs
by Molly Peeples 27 Jul '16

27 Jul '16

Hi folks, I am trying to read in a Gadget output that’s split into 16 hdf5 files (fwiw, it’s an EAGLE output, and so “should” be similar to the OWLS format). I need to be able to analyze / render the entire output, not just one of the pieces, but I haven’t been able to figure out how to actually load them (akin to how for Enzo yt figures out that there are a lot of cpu outputs in a directory). I have taken a look at http://yt-project.org/doc/cookbook/owls_notebook.html#owls-notebook, but even there in the example, it’s just reading in the one output and ignoring the other 7 in the example tarball. And there I was having trouble tracking down what n_ref and over_refine_factor refer to. Interestingly, if I load just the single hdf5s, I can get ProjectionPlots to work but not SlicePlots (which insist there’s “zero dynamic range” with “Min = Max = 0.00000”.) FWIW, yt.__version__ gives me 3.3.1. (And major thanks to Nathan for getting that installation to go smoothly!!) Suggestions? —Molly

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emission weighted temperature profile
by Mateusz Ruszkowski 27 Jul '16

27 Jul '16

Hi, [apologies if you received this twice; I have problems with my e-mail[ I am trying to plot an emission-weighted temperature profile. The relevant part of my script and the error message are attached below. Does anybody have an idea why this is not working? Thanks, Mateusz ——— part of yt script ——— from yt.analysis_modules.spectral_integrator.api import add_xray_emissivity_field […] def my_temp(field, data): return data['flash', 'temp'] ds=yt.load("/nobackupnfs2/mruszkow/halo_hdf5_plt_cnt_%04i"%i) xray_fields = add_xray_emissivity_field(ds, with_metals=False, constant_metallicity=1.0, e_min=0.5, e_max=10.0, filename="apec_emissivity.h5") ds.add_field(("flash", "my_temp"), units="code_temperature", function=my_temp) sp = ds.sphere([0.0,0.0,0.0], rmax) prof = yt.Profile1D(sp, "radius", xbins, prof_min, prof_max, True, weight_field="xray_emissivity_0.5_10_keV") #"cell_mass") prof.add_fields(["my_temp"]) ——— error message ——— yt : [INFO ] 2016-07-25 17:20:54,022 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2016-07-25 17:20:54,023 Loading emissivity data from apec_emissivity.h5. yt : [INFO ] 2016-07-25 17:20:54,023 b'X-ray emissivity data calculated with APEC v. 2.0.2 on 06/24/2014 by John ZuHone.' yt : [INFO ] 2016-07-25 17:20:54,023 X-ray emissivity data version: 1. yt : [WARNING ] 2016-07-25 17:20:56,114 Could not find a field for "H_number_density". Assuming primordial H mass fraction. Traceback (most recent call last): File "temperature2.py", line 64, in <module> prof = yt.Profile1D(sp, "radius", xbins, prof_min, prof_max, True, weight_field="xray_emissivity_0.5_10_keV") #"cell_mass") File "/home3/mruszkow/yt/yt/data_objects/profiles.py", line 410, in __init__ super(Profile1D, self).__init__(data_source, weight_field) File "/home3/mruszkow/yt/yt/data_objects/profiles.py", line 92, in __init__ weight_field = self.data_source._determine_fields(weight_field)[0] File "/home3/mruszkow/yt/yt/data_objects/data_containers.py", line 985, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/home3/mruszkow/yt/yt/data_objects/static_output.py", line 616, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('io', 'xray_emissivity_0.5_10_keV')' in halo_hdf5_plt_cnt_0010.

2 2

not able to see anything in notebook
by Ritam Mallick 26 Jul '16

26 Jul '16

Dear Users, I have installed yt in my desktop. however when I am trying to import yt and load or see anything in the notebook app I cannot see anything. The message is as follows .. ritam@ritam:~/yt/doc/source/quickstart$ yt notebook /home/ritam/yt-conda/lib/python2.7/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`. "`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning) You must choose a password so that others cannot connect to your notebook. Enter password: Verify password: If you would like to use this password in the future, place a line like this inside the [yt] section in your yt configuration file at ~/.yt/config notebook_password = sha1:1631cf9cf288:25f1cbe46746e0d25aed15a26deec2d048ff3570 *************************************************************** The notebook is now live at: http://127.0.0.1:8888/ Recall you can create a new SSH tunnel dynamically by pressing ~C and then typing -L8888:localhost:8888 where the first number is the port on your local machine. If you are using 8888 on your machine already, try -L8889:localhost:8888 *************************************************************** [I 10:37:04.487 NotebookApp] Serving notebooks from local directory: /home/ritam/yt/doc/source/quickstart [I 10:37:04.487 NotebookApp] 0 active kernels [I 10:37:04.487 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/ [I 10:37:04.487 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). import yt ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030") It is just running and running and not showing anything. Friends, please help me in this regard. Thanks in advance. Ritam

1 1

installation problem
by Ritam Mallick 22 Jul '16

22 Jul '16

Dear all, I am trying to install yt in my desktop (Ubuntu 15.04). However it shows this error (last few lines of the yt_install.log) running install_scripts copying build/scripts-2.7/hg -> /home/ritam/yt-x86_64/bin changing mode of /home/ritam/yt-x86_64/bin/hg to 775 running install_egg_info Writing /home/ritam/yt-x86_64/lib/python2.7/site-packages/mercurial-3.4-py2.7.egg-info using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: No module named _ssl! using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: No module named _ssl! abort: repository /home/ritam/yt-x86_64/src/yt-hg/ not found! 2016-07-22 17:28:23 URL:https://bootstrap.pypa.io/get-pip.py [1524722/1524722] -> "get-pip.py" [1] Traceback (most recent call last): File "get-pip.py", line 19177, in <module> main() File "get-pip.py", line 194, in main bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpDR_d0M/pip.zip/pip/__init__.py", line 16, in <module> File "/tmp/tmpDR_d0M/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpDR_d0M/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpDR_d0M/pip.zip/pip/wheel.py", line 39, in <module> File "/tmp/tmpDR_d0M/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpDR_d0M/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler Hope to get some help.

2 1

Clump surface pressure
by John Regan 21 Jul '16

21 Jul '16

Hi All, I was hoping to calculate the surface pressure on the surface of a clump. I see that there is a way to do this with surfaces at the moment in YT probably by doing something like: mysurf.calculate_isocontour_flux(*"density"*, *some_value*, *r_x*, *r_y*, *r_z*, *"pressure"*) So while that has a fair chance of working for a surface? Is there any way to get a clump to do the same? Any tips/advice greatly appreciated! Cheers, John

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yt-users July 2016