yt-users October 2016

yt-users@python.org

28 participants
27 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

Issue loading data with yt
by Matthew Robert Brinson 02 Nov '16

02 Nov '16

Hi yt-users, Let’s try this again. The file I sent the first time was too large. I’m using yt version 3.3.1, and I’ve recently encountered an issue loading data correctly. I’m running SPH simulations of white dwarf mergers and want to know what the mass fractions of different elements are at different times. I have two files that contain the data: 1) a tipsy file, 2) and a text file that contains the mass fraction values of helium-4. The tipsy file loads just fine and I’m able to access the information from the helium file once the tipsy file is loaded. For some reason though, when I have more than 262144 particles in my simulation, yt does not load the helium mass fraction values correctly anymore. I’ve initialized all particles to have a 4% helium mass fraction, and all of the particles up to and including the particle indexed by 262143 have this value, but after that the particles all have 0% according to yt. I’ve checked the helium files directly and all values are at 4%. I’m confused as to why yt would stop loading values correctly after a certain point. I’ve included two tipsy files as well as their corresponding helium mass fraction files. I have also written a script called visualization_test_script.py that makes scatter plots of the white dwarfs showing particles that have correct and incorrect values of helium. I can send more tipsy files if necessary, but they are too large to send any more here. Thanks, Matt

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Issue loading data with yt
by Matt Brinson 31 Oct '16

31 Oct '16

Hi ht-users, Let’s try this again. The file I sent the first time was too large. I’m using yt version 3.3.1, and I’ve recently encountered an issue loading data correctly. I’m running SPH simulations of white dwarf mergers and want to know what the mass fractions of different elements are at different times. I have two files that contain the data: 1) a tipsy file, 2) and a text file that contains the mass fraction values of helium-4. The tipsy file loads just fine and I’m able to access the information from the helium file once the tipsy file is loaded. For some reason though, when I have more than 262144 particles in my simulation, yt does not load the helium mass fraction values correctly anymore. I’ve initialized all particles to have a 4% helium mass fraction, and all of the particles up to and including the particle indexed by 262143 have this value, but after that the particles all have 0% according to yt. I’ve checked the helium files directly and all values are at 4%. I’m confused as to why yt would stop loading values correctly after a certain point. I’ve included two tipsy files as well as their corresponding helium mass fraction files. I have also written a script called visualization_test_script.py that makes scatter plots of the white dwarfs showing particles that have correct and incorrect values of helium. I can send more tipsy files if necessary, but they are too large to send any more here. Thanks, Matt

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[ANN] yt-3.3.2 released
by Nathan Goldbaum 28 Oct '16

28 Oct '16

The yt community is proud to announce the release of yt 3.3.2! yt (http://yt-project.org) is an open source, community developed toolkit for the analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical and nuclear engineering simulations. yt 3.3.2 is a bugfix release that includes a number of fixes and enhancements for issues discovered after the release of yt 3.3.1. We urge all yt 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: Corentin Cadiou Nathan Goldbaum Cameron Hummels Suoqing Ji Ben Keller Chang-Goo Kim Kacper Kowalik Alex Lindsay Andrew Myers John Regan Mark Richardson Rafael Ruggiero Hsi-Yu Schive Britton Smith Matthew Turk John Wise Michael Zingale John ZuHone A summary of changes in this release, along with the number of the pull request implementing the change follows below: * Ensure package data files are installed to the correct location (PR 2425) * Ensure particle profile date are interpreted in the correct units for Enzo data (PR 2423) * Work around an issue with reading FLASH 2.5 data using the latest release of h5py. (PR 2421) * Update docstrings for RockstarHaloFinder (PR 2416) * Convert the axis argument of the argmax function to a list if it is not one already (PR 2414) * Make the annotate_clear callback return an instance of the plot for improved user experience in the Jupyter notebook (PR 2413) * Explicitly use integer divion to avoid reading in incorrect grid data in python3 (PR 2412) * Suppress logging when searching for datasets in a simulation time series (PR 2409) * Update instructions on how to set the log level for the yt logger in the documentation (PR 2400) * Various bugfixes for the light ray functionality. These fixes will impact answers generated by the Trident code. (PR 2321, PR 2323, PR 2342, PR 2344, PR 2345, PR 2399) * Don't use /apjs macro in suggested citation (PR 2398) * Add new fields to the list of known fields in the Enzo frontend (PR 2397) * Update configuration for nose so that absolute paths to tests work correctly (PR 2395) * Add mention of ytree to the merger tree documentation (PR 2393) * Install netcdf by default in the install script (PR 2389) * Fix a units issue in the implementation of ds.box (PR 2387) * Disable a randomly failing test (PR 2384) * Fix zoom for the perspective lens (PR 2381) * Fix test failures in a 32 bit build of yt (PR 2380) * Avoid a zero division error in the volume renderer (PR 2379, PR 2388) * Don't take the absolute value of the redshift for the timestamp PlotWindow callback (PR 2373) * Don't try to read non-existent tipsy auxiliary files (PR 2370) * Fix a type issue that causes load_octree to crash (PR 2362) * Performance improvements for the get_vertex_centered_data function (PR 2341) * Performance improvements for the particle_trajectories analysis module (PR 2337) *The LaTeX representation of yt units with numeric multiplicative factors has been improved (PR 2310) * The annotate_cell_edges PlotWindow callback now produces output that is more uniform as a function of image resolution (PR 2307) * Fix a number of issues in the example skeleton frontend (PR 2357) * Mention the availability of demo.use.yt in the quickstart guide (PR 2358) * A realoaded ytdata dataset generated from a profile object can now be plotted with ProfilePlot or PhasePlot (PR 2357) * Make smoothed_covering_grid work correctly with 1D and 2D data. (PR 2354) * Fail more gracefully if yt loads a FLASH dataset with accompanying particle file and the particle file is not from the same simulation time as the plot file. (PR 2353) * Fix an issue with locally defined derived fields not generating correct colorbar labels (PR 2351) * Avoid mutating a YTArray passed into the YTArray initializer (PR 2347) * RAMSES fields and parameters with units of time are now read in correctly for cosmological simulations (PR 2346, PR 2374) * Print a nicer error message when trying to create a profile object that mixes particle and mesh fields (PR 2338) * Ensure the FixedResolutionBuffer object associated with PlotWindow plots is regenerated before it is used again if it is invalidated. (PR 2335) * Fix an issue that would cause incorrect units to be used if units are passed in at dataset load time with units_override (PR 2334, PR 2407) * Add gravitational_potential as a known field in the Athena frontend (PR 2333) * Make 'metallicity' a known field in the stream frontend (PR 2331) * Prevent a segmentation fault in the volume renderer by accounting for round-off error. (PR 2328) * Minor fix for the documentation of the Streamline functionality (PR 2317) * Spelling fixes in the PlotWindow documentation (PR 2313) * Add metadata for a number of new castro fields (PR 2312) * Fix an issue with converting units from the latest version of the Pint package to yt units (PR 2309) * Halo properties written out by rockstar-galaxies can now be read in by the rockstar frontend (PR 2306) * The git hash of the version of castro used to produce a castro dataset can now be queried (PR 2305) * Fix a bug in scene.show() that might cause volume rendering images to now show up inline in the notebook (PR 2304) * Various fixes for the install script (PR 2308, PR 2316, PR2311, PR 2327)

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remap spherical geometry on cartesian
by Andrea Negri 27 Oct '16

27 Oct '16

Hi all, I'm still struggling in porting the my ZEUS data in spherical coordinates in yt. After many tests, I decided that it would by a good idea to interpolate all my arrays from the spherical (non uniform) grid to an AMR grid in cartesian (it will help me also with other software that accepts only cartesian coordinates). I wrote a python program to create an octree, but it is quite unefficient. Than, I read that it is possible to create an octree with yt. What I REALLY would like to do is to compute the octree, save all grids, all the levels in the GDF format, than with a script open the GDF format and insert in every grid the interpolated density, energy etc... I'm able to create the octree (or at least I think!) using the attached script, but I don't know how to save it in the GDF format. Could you help me? Many thanks, Andrea

1 0

divergence of velocity field in yt
by turhan nasri 27 Oct '16

27 Oct '16

Hi people, I wish to see the sliceplots of "divergence of velocity" fields in yt. I see yt has an example of how to derive gradient of a scalar field , is there any example to show how to derive new field for divergence too ? Best Turhan

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YT-3.3.1 : selecting cells in a sphere
by Vincent Picouet 27 Oct '16

27 Oct '16

Hi, I am getting an issue with a very basic YT code: I am using the 3.3.1 version and I can not access the cells contained in a sphere (it returns all the cells of the ENZO simulation): The YT cookbook explains that to access the different fields (for example the x position) of the cells contained in a sphere one must code : ds.sphere[(0.5,0.5,0.5),0.1)][‘x’] … But it gives me exactly the same results of ds.all_data().[‘x’] which is a 100M cells’ list. Do you have an idea about selecting only the sphere region easily? Thanks Vincent

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Regarding MergerTree() parameters.
by Reju Sam John 26 Oct '16

26 Oct '16

Dear all, I would like to get few clarification on yt.analysis_modules.halo_merger_tree.merger_tree.MergerTree() 1) MergerTree() has a parameter halo_finder_threshold. Does this something synonym to virial overdensity(like M200 or R200 ) ? 2) FOF_link_length parameter for halo_finder_function = FOFHaloFinder. The default value is 0.2. My doubt is, 0.2 is in which unit ? Is it in code unit or Mpc ? And also halo_finder_function = HaloFinder and halo_finder_function = FOFHaloFinder are giving entirely different value for the Group Mass in the MergerHalo.out (a difference of more than one order of magnitude) thank you. -- Reju Sam John

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Error in Rockstar Halo Finding
by Reju Sam John 26 Oct '16

26 Oct '16

Hi all, I am trying to run Rockstar Halo Finding with the following code. from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder #find all of our simulation files files = glob.glob("RD*/*hierarchy") #hopefully the file name order is chronological files.sort() print files ts = TimeSeriesData.from_filenames(files[:]) rh = RockstarHaloFinder(ts) rh.run() but I am getting the following error. File "rockstar_halo_finding.py", line 14, in <module> rh = RockstarHaloFinder(ts) File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 220, in __init__ self.pool, self.workgroup = self.runner.setup_pool() File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 102, in setup_pool (self.num_writers, "writers") ] File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 325, in from_sizes pool.add_workgroup(size, name = name) File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 293, in add_workgroup group = self.comm.comm.Get_group().Incl(ranks) AttributeError: 'NoneType' object has no attribute 'Get_group' could you please explain what is going wrong here ? Thank you. -- Reju Sam John

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yt-users October 2016