Mailman 3 December 2016 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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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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RAMSES multiple sims memory issue
by Thor Andreas Seiff Ellewsen 02 Jan '17

02 Jan '17

Hi all, I'm working on a project where I'm comparing different RAMSES simulations. However I'm running into a problem with memory. It seems that yt loads the whole simulation into memory even though I'm only interested in a number of dark matter halos which I have the coordinates for. It also seems like it doesn't drop the first simulation out of memory when I'm done making the figures I want for that one. This quickly fills up the memory. You can find the relevant parts of my code at the pastebin at http://paste.yt/p4946.html I'm running yt version 3.3.2 What am I doing wrong? Also, is there a way to change the axis names? I'm making some dark matter density profiles using the ('deposit','io_density') field and this gives IO Density on the y axis, but I just want it to say Dark matter density so my readers actually understand what I'm talking about. Thanks for helping Best, Andreas Ellewsen

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Accessing scalar fields in ramses
by mohammad safarzadeh 21 Dec '16

21 Dec '16

Hi all, I have been running zoom simulations with with two scalar fields, 1-metallicity, 2-rpgas. Therefore I run ramses compiled with NVAR=8. when I load the dataset with YT, I see “metallicity”,“var6” and “var7” where var6 and 7 are for Rpgas and zoom sim (as ramses treats zoom sim itself as a scalar variable). When I turned on the delayed cooling, which is yet another scalar field in ramses, I compiled and run the code with NVAR=9. However, YT still sees two variables and I don’t see any “var8” in the field_list. In other words I have three scalar fields but YT is not detecting them. Is there a way around this? Thank you very much, All best, Mohammad -- Mohammadtaher Safarzadeh, Ph.D. http://www.mtsafarzadeh.com

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ANN: Release of Trident--A Synthetic Spectral Generation Code
by Cameron Hummels 13 Dec '16

13 Dec '16

We are pleased to announce the official release of Trident, a universal, Python-based, open-source tool for post-processing hydrodynamics simulations to produce synthetic absorption spectra and related data. Trident's features include: --Creates absorption-line spectra for any trajectory through a simulated dataset --Reproduces the spectral characteristics of common spectrographs like COS --Operates across the ultraviolet, optical and infrared using customizable absorption line lists --Traces simulated physical structures directly to spectral features --Approximates the presence of ion species absent from the simulation outputs --Generates column density maps for any ion --Provides support for all major astrophysical hydrodynamical codes. --Fully parallelizable using MPI and MPI4PY --Built as an extension of the yt analysis code <http://yt-project.org> For more information about its features, including a video demonstrating its use, and links to its documentation and source code, please see our website: http://trident-project.org . There is an accompanying method paper that was released today on the arXiv available at: https://arxiv.org/abs/1612.03935 Please spread word of this announcement to others who might be interested. The Trident Developer Team-- Cameron Hummels, Britton Smith, Devin Silvia -- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org

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Volume render
by Sushilkumar 13 Dec '16

13 Dec '16

Dear yt: I am trying to do volume rendering for my data and create a time lapse movie. Is there a way to extract and put lower and upper bound while volume render? This is to maintain a consistency between frames. My code is below Thanks in advance import yt import numpy as np import matplotlib.pylab as pl from yt.visualization.api import Streamlines from yt.units import km from mpl_toolkits.mplot3d import Axes3D ms = 52728000 vector_max=ms-(ms/3) ms1=ms-vector_max dims = (260,260,260) x = np.genfromtxt("/home/sushilkumar.sreekuma/Desktop/MODEL5/UPDATE/Expl_Bt696.mtx",skip_header=2,usecols=1, dtype="f8") x = x.reshape((17576000, 3), order="F") field1 = x[:,2].reshape(dims, order="F") field2 = x[:,1].reshape(dims, order="F") field3 = x[:,0].reshape(dims, order="F") data = dict(field_z = field1, field_y = field2, field_x = field3) bbox = np.array([[-130, 129], [-130, 129], [-130, 129]]) pf = yt.load_uniform_grid(data, dims, km, bbox=bbox, nprocs=1) im, sc = yt.volume_render(pf,'field_x',fname='B_rendering_t0696.png',sigma_clip=6) sc.camera.width = (150, 'km') sc.camera.switch_orientation() # Save the zoomed in rendering sc.save('B_zoomed_rendering_t0696.png') On Mon, Dec 12, 2016 at 12:54 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. ANN: yt 3.3.3 release (Cameron Hummels) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Dec 2016 10:34:53 -0800 > From: Cameron Hummels <chummels(a)gmail.com> > To: "yt-dev(a)lists.spacepope.org" <yt-dev(a)lists.spacepope.org>, > Discussion of the yt analysis package < > yt-users(a)lists.spacepope.org> > Subject: [yt-users] ANN: yt 3.3.3 release > Message-ID: > <CACyTu7EM43epAiQkO+vLeq2oc92f5hvw+KM-5+cUdPThTxe= > MA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > We are proud to announce the release of yt 3.3.3! > > Version 3.3.3 is a regularly scheduled bugfix release including fixes for a > number of issues reported since the release of yt 3.3.2. We urge all users > to update to the latest version. > > If your python installation is managed via conda, update following: > > $ conda update -c conda-forge yt > > If your python installation is managed via pip, update following: > > $ pip install -U yt > > Finally, if you manage your yt installation by running out of a clone of > the yt mercurial repository, update following: > > $ yt update > > We would like to thank the following people for their contributions to this > release: > > Nathan Goldbaum > Cameron Hummels > Ben Keller > Kacper Kowalik > Jonah Miller > Andrew Myers > Hsi-Yu Schive > Britton Smith > Matthew Turk > John Wise > John ZuHone > > > A summary of changes in this release, along with the number of the pull > request implementing the change follows below: > > Additional docstrings for unstructured mesh data. See PR 2403 > <https://bitbucket.org/yt_analysis/yt/pull-requests/2403/some-hopefully- > illuminating-docstrings-for/diff> > . > > Speedup in clump finding. See PR 2426 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2426/opt-typedef-array-returned-in/diff> > . > > Speedup in tests. See PR 2427 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2427/use-slighlty-smaller-objects-for-certain/diff> > . > > Bugfixes and docs for Tipsy data. PR 2430 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2430/tipsy-correct-auxiliary-file-footer-skip/diff> > , PR 2431 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2431/clarify-the-use-of-cosmology_parameters-in/diff> > . > > Bugfix in Ramses time calculation. PR 2433 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2433/bugfix-explicitly-use-integer-division-in/diff> > . > > Bugfix in octree indexing. PR 2434 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2434/bugfix-explicitly-use-integer-division-in/diff> > . > > Fixing behavior of ProfilePlots and Profiles PR 2437 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2437/bugfix-fix-rich-display-of-profileplot-in/diff> > , PR 2448 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2448/bugfix-more-careful-treatment-of-profile/diff> > . > > Bugfix for EPSWritter handing dicts in PlotsWindow instances. PR 2440 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2440/updating-eps_writer-to-handle-a-plotwindow/diff> > . > > Ensuring ion fields utilize dataset's metal-specific fields PR 2442 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2442/making-nuclei-density-fields-more-robust/diff> > . > > Assure no orphaned mercurial processes PR 2449 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2449/interact-with-mercurial-repositories-using/diff> > . > > Adding checks for bad values in AbsorptionSpectrum PR 2450 > <https://bitbucket.org/yt_analysis/yt/pull-requests/2450/adding-check-for- > negative-column-densities/diff> > . > > Bugfix in geographic handler PR 2452 > <https://bitbucket.org/yt_analysis/yt/pull-requests/2452/fixing-x-y-axis- > confusion-in-the/diff> > . > > Bringing gadget data more inline with other SPH datasets PR 2456 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2456/enabling-gadget-frontend-to-alias/diff> > , PR 2436 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2436/bugfix-use-integer-division-in-gadget-io/diff> > . > > Bugfix when OpenMP unavailable PR 2458 > <https://bitbucket.org/yt_analysis/yt/pull-requests/2458>. > > Enable light_ray_solution saved to actual LightRay class PR 2460 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2460/save-light-ray-solution-to-dataset/diff> > . > > Assure path uses dataset's own unit system. PR 2462 > <https://bitbucket.org/yt_analysis/yt/pull-requests/ > 2462/path-unit-should-use-datasets-unit-system/diff> > . > > Cameron Hummels, > On behalf of the yt development team > > -- > Cameron Hummels > NSF Postdoctoral Fellow > Department of Astronomy > California Institute of Technology > http://chummels.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20161212/63583846/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 106, Issue 7 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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ANN: yt 3.3.3 release
by Cameron Hummels 12 Dec '16

12 Dec '16

We are proud to announce the release of yt 3.3.3! Version 3.3.3 is a regularly scheduled bugfix release including fixes for a number of issues reported since the release of yt 3.3.2. We urge all users to update to the latest version. If your python installation is managed via conda, update following: $ conda update -c conda-forge yt If your python installation is managed via pip, update following: $ pip install -U yt Finally, if you manage your yt installation by running out of a clone of the yt mercurial repository, update following: $ yt update We would like to thank the following people for their contributions to this release: Nathan Goldbaum Cameron Hummels Ben Keller Kacper Kowalik Jonah Miller Andrew Myers Hsi-Yu Schive Britton Smith Matthew Turk John Wise John ZuHone A summary of changes in this release, along with the number of the pull request implementing the change follows below: Additional docstrings for unstructured mesh data. See PR 2403 <https://bitbucket.org/yt_analysis/yt/pull-requests/2403/some-hopefully-illu…> . Speedup in clump finding. See PR 2426 <https://bitbucket.org/yt_analysis/yt/pull-requests/2426/opt-typedef-array-r…> . Speedup in tests. See PR 2427 <https://bitbucket.org/yt_analysis/yt/pull-requests/2427/use-slighlty-smalle…> . Bugfixes and docs for Tipsy data. PR 2430 <https://bitbucket.org/yt_analysis/yt/pull-requests/2430/tipsy-correct-auxil…> , PR 2431 <https://bitbucket.org/yt_analysis/yt/pull-requests/2431/clarify-the-use-of-…> . Bugfix in Ramses time calculation. PR 2433 <https://bitbucket.org/yt_analysis/yt/pull-requests/2433/bugfix-explicitly-u…> . Bugfix in octree indexing. PR 2434 <https://bitbucket.org/yt_analysis/yt/pull-requests/2434/bugfix-explicitly-u…> . Fixing behavior of ProfilePlots and Profiles PR 2437 <https://bitbucket.org/yt_analysis/yt/pull-requests/2437/bugfix-fix-rich-dis…> , PR 2448 <https://bitbucket.org/yt_analysis/yt/pull-requests/2448/bugfix-more-careful…> . Bugfix for EPSWritter handing dicts in PlotsWindow instances. PR 2440 <https://bitbucket.org/yt_analysis/yt/pull-requests/2440/updating-eps_writer…> . Ensuring ion fields utilize dataset's metal-specific fields PR 2442 <https://bitbucket.org/yt_analysis/yt/pull-requests/2442/making-nuclei-densi…> . Assure no orphaned mercurial processes PR 2449 <https://bitbucket.org/yt_analysis/yt/pull-requests/2449/interact-with-mercu…> . Adding checks for bad values in AbsorptionSpectrum PR 2450 <https://bitbucket.org/yt_analysis/yt/pull-requests/2450/adding-check-for-ne…> . Bugfix in geographic handler PR 2452 <https://bitbucket.org/yt_analysis/yt/pull-requests/2452/fixing-x-y-axis-con…> . Bringing gadget data more inline with other SPH datasets PR 2456 <https://bitbucket.org/yt_analysis/yt/pull-requests/2456/enabling-gadget-fro…> , PR 2436 <https://bitbucket.org/yt_analysis/yt/pull-requests/2436/bugfix-use-integer-…> . Bugfix when OpenMP unavailable PR 2458 <https://bitbucket.org/yt_analysis/yt/pull-requests/2458>. Enable light_ray_solution saved to actual LightRay class PR 2460 <https://bitbucket.org/yt_analysis/yt/pull-requests/2460/save-light-ray-solu…> . Assure path uses dataset's own unit system. PR 2462 <https://bitbucket.org/yt_analysis/yt/pull-requests/2462/path-unit-should-us…> . Cameron Hummels, On behalf of the yt development team -- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org

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Accessing some derived fields
by Prachi Parihar 07 Dec '16

07 Dec '16

Hi all, I am trying to compute vorticity for a fire snapshot. I've put down a sphere (sp), and can access some other derived fields, but for some reason things like vorticity give me the following error. Does anyone have suggestions as to what I'm doing wrong? >>> sp['gas','velocity_magnitude'] YTArray([ 53724618.56288539, 48756921.3449135 , 46197475.78549621, ..., 53664392.60568497, 46881343.68564206, 50050673.058614 ]) cm/s >>> sp['gas','vorticity_x'] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 281, in __getitem__ self.get_data(f) File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1295, in get_data self._generate_fields(fields_to_generate) File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 1315, in _generate_fields fd = self._generate_field(field) File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 318, in _generate_field tr = self._generate_fluid_field(field) File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 336, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ data_objects/data_containers.py", line 359, in _generate_spatial_fluid for i, chunk in enumerate(chunks): File "/home/prachi/anaconda2/lib/python2.7/site-packages/yt/ geometry/particle_geometry_handler.py", line 179, in _chunk_spatial g = og.retrieve_ghost_zones(ngz, [], smoothed=True) AttributeError: 'ParticleOctreeSubset' object has no attribute 'retrieve_ghost_zones'

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Last Week to Apply for Python in Astronomy 2017
by Stuart Mumford 05 Dec '16

05 Dec '16

Hello all, This a quick (and final) reminder that the deadline for applications to Python in Astronomy 2017 is this *Friday 9th December*. The conference will be held on 8th - 12th May 2017 at the Lorentz Center in Leiden, the Netherlands. Please fill out this form <https://docs.google.com/forms/d/e/1FAIpQLSfFvzolQvW5PJRbgIoPs73t4LgMIDNX2lX…> to apply. The Python in Astronomy conferences aim to bring together a wide variety of people who currently use, develop or teach people about Python packages in the context of all forms of Astronomy. Participant selection will be made with the goal of growing the Python in Astronomy community and we particularly encourage requests to attend from junior astronomers and people who are new to contributing to open source software. This conference is neither intended to be an introduction to Python bootcamp nor only for expert-level Python developers, but we do expect all participants to have at least a basic familiarity with Python. Please fill out the application and indicate the level of financial support you will likely require in order to attend. Once the participants have been selected, we’ll get back in touch with everyone about their specific financial support requirements. See http://openastronomy.org/pyastro/2017/ for more information. Stuart Mumford, SOC Chair Matt Craig Kelle Cruz Daniela Huppenkothen Abigail Stevens Erik Tollerud

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