yt-users June 2016

yt-users@python.org

26 participants
30 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 22 Aug '16

22 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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getting abundance of elements contained within a sphere through Profile1D funcion
by tazkera haque 30 Jun '16

30 Jun '16

Hi, I am trying to find abundance of C contained within a sphere through the Profile1D function in yt. I tried something like this: *ds=yt.load(filename)* * sp = ds.sphere("max", (10.0, 'kpc'))* * profile = yt.Profile1D(sp, "x", 32, rmin, rmax, False, weight_field=None)* * profile.add_fields(["cell_mass"])* * profile.add_fields(["c12 "])* * profile.add_fields(["x"])* *print profile ["cell_mass"].sum()/Msun* *print profile ["c12 "]*["cell_mass"].sum()/Msun* and got the following error: * File "profile_1D.py", line 74, in <module>* * print profile ((["c12 "]*["cell_mass"]).sum())/Msun* *TypeError: can't multiply sequence by non-int of type 'list'* *is there any way I can calculate the C12 abundance here?* *Best* *Tazkera*

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Trouble installing yt
by Elliot Eckholm 30 Jun '16

30 Jun '16

I am very new to yt and am having trouble installing it. I am running on a Macbook pro 2011 with OS X El Capitan version 10.11.5 This steps I took: $ hg clone https://bitbucket.org/yt_analysis/yt $ cd yt $ chmod +x ./doc/install_script.sh $ ./doc/install_script.sh After sometime installing... I get this: ******************************************** FAILURE REPORT: ******************************************** from //System/Library/Frameworks/CoreGraphics.framework/Headers/CoreGraphics.h:11, from //System/Library/Frameworks/ApplicationServices.framework/Headers/ApplicationServices.h:35, from //System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:24, from Include/pymactoolbox.h:10, from Python/mactoolboxglue.c:27: //System/Library/Frameworks/CoreGraphics.framework/Headers/CGFont.h:53:1: error: initializer element is not constant static const CGFontIndex kCGGlyphMax = kCGFontIndexMax; ^ Makefile:1286: recipe for target 'Python/mactoolboxglue.o' failed make: *** [Python/mactoolboxglue.o] Error 1 ******************************************** ******************************************** Failure. Check /Users/elliote/Desktop/Theia_Streaming_Tutorial/yt/yt-x86_64/yt_install.log. The last 10 lines are above. Does anyone have any ideas on how I can go about fixing this? Thanks!

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SPH from generic particle stream?
by Jonah Miller 28 Jun '16

28 Jun '16

Hi yt-users, I'm trying to play around with yt for SPH type data (there's no frontend for this code). I found out how to load generic particle data via the load_particle_data stream (http://yt-project.org/docs/dev/examining/generic_particle_data.html#generic…) and I found some information on SPH type data (http://yt-project.org/doc/analyzing/fields.html#sph-fields) but I can't seem to figure out how to tell yt that I have a smoothing length and a particle I want to smooth. Is there a way to do this? I attach a non-working script showing roughly what I'm trying to do. Thanks in advance! Best, Jonah

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Error: Particle Bounds
by Adrianna Perez 27 Jun '16

27 Jun '16

To whom it may concern, I am having trouble loading GIZMO data to make a simple slice plot and this is the error I get: yt.utilities.exceptions.YTDomainOverflow: Particle bounds (-934.41559, -727.99188, -1092.047) and (509.55978, 797.46954, 1034.1028) exceed domain bounds [ 0. 0. 0.] code_length and [ 10000. 10000. 10000.] code_length Any help would be really useful. Please send me any questions you may have. Please and thank you, Adrianna Perez

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Reviewing pull requests
by Stephanie Tonnesen 27 Jun '16

27 Jun '16

Hi yt-users, So I am using the developers yt-conda version of yt. I am trying to review a pull request, but have no idea what I am doing. All I ever do is yt update I literally just broke yt 5 days ago, so I am a bit unwilling to just poke around trying out random hg commands to see what happens. Is this what I am supposed to do once I have activated yt? hg clone https://bitbucket.org/yt_analysis/ytcd yt hg update yt python setup.py install --user --prefix= And *if* this is right, how do I grab a specific change set? Thanks so much! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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Projection disagrees with original data.
by Hansheng Chen 27 Jun '16

27 Jun '16

Hello yt users, I have a question about projection. I used ds.proj() and to_frb() to get an image array of the projected 'Electron_Density' of an entire dataset. I multiplied the mean of projected 'Electron_Density' by the entire area of x-y plane and got a sum of total mass of electrons. Then, I used ds.all_data() and mean() to get the mean of 'Electron_Density' in 3-dimensional. I multiplied the mean by the volume of the entire box of the dataset and got another sum of total mass of electrons. However, this sum did not match the sum I got from the projected 'Electron_Density' previously. Here are the codes I used: import yt import numpy as np ds = yt.load("redshift0100/redshift0100") print("Redshift =", ds.current_redshift) p = yt.ProjectionPlot(ds, 2, 'Electron_Density') density_image = p.frb['Electron_Density'] ed = density_image['Electron_Density'].convert_to_cgs() ed_ndarr = ed.to_ndarray() sum1 = ed_ndarr.mean() * ((105.82 * 3.085677581e+24)**2) print(sum1) dd = ds.all_data() ed_3d = dd['Electron_Density'].convert_to_cgs() sum2 = ed_3d.mean() * ((105.82 * 3.085677581e+24)**3) print(sum2) (105.82 * 3.085677581e+24) is the width of entire box in cm. I think sum1 and sum2 should be close to each other, but the result was that the two values did not match with each other. Is there any problem in the codes I used to get the values of sum1 and sum2? Could some one give me some help? Thank you very much! Sincerely, Hansheng

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creating gradient of a field as a derived field
by turhan nasri 27 Jun '16

27 Jun '16

Hi yt people, I need a little help creating a derived field which will return me the negative gradient of gravitational potential *@derived_field(name = "gradient_gravpot", units = " cm/s**2")* *def _gradient (field, data):* * G = add_gradient_fields(("gas"," gravitational_potental"))* * return (- data["gravitational_potential_gradient_x"])* and I got this error *NameError: global name 'add_gradient_fields' is not defined* please suggest the right method to define the field. thanks Best Turhan

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yt-users June 2016