yt-users June 2018

yt-users@python.org

16 participants
17 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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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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extracting regions
by ｔyuta 08 Jul '18

08 Jul '18

Dear yt-users, Hi, I want to know about the function "extract_connected_sets". I want to extract SuperNova enriched bubbles (which I define as Z > -4 or something) and analyze its size or mass or some other values. I'm working with cosmological simulation by enzo, and there are many SN enriched bubbles. What I need is the set of "bubble regions" of (probably) YTRegions. For this purpose, it seemed to me that "extract_connected_sets" would be the perfect function, but I don't understand what this object is, or how I can analyze the object, because when I tried projection plot of the objects, nothing appeared. Could you tell me how I can use "extract_connected_sets"? Or, is there any other way to extract SN enriched region? Best, YT

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Question about star particle
by ｔyuta 28 Jun '18

28 Jun '18

Dear yt users, Hi, I want to ask about star particles in enzo simulation. I want to know whether "star particle filter" only give me "alive" star particles or also counts "dead" particles (which have exploded in the past). I defined the "star particle" with particle filter like this: import yt from yt.data_objects.particle_filters import add_particle_filter def stars(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 2 return filter def DMparticles(pfilter, data): filter = data[(pfilter.filtered_type, "particle_type")] == 1 return filter yt.add_particle_filter("Stars", function=stars, filtered_type='io', requires=["particle_type"]) yt.add_particle_filter("DMparticles", function=DMparticles, filtered_type='io', requires=["particle_type"]) ds = yt.load("~/IsolatedGalaxy/galaxy0030/galaxy0030") ds.add_particle_filter('Stars') ds.add_particle_filter('DMparticles') ad = ds.all_data() stellar_mass = ad[("Stars", "particle_mass")].in_units('Msun') print(stellar_mass) Does this "stellar_mass" contain both alive and dead stars ? Best, Y.T.

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Annotating BH particles on SlicePlots
by Sam Patrick 19 Jun '18

19 Jun '18

Hi all, I'm trying to annotate BH particles on top of a regular yt SlicePlot. I'm loading from an Enzo dataset and using yt version 3.3.1, the plot field and width in parsecs are given as command line arguments (I tried using density and 3.0). Here is the script I'm working with: import yt import sys from yt.units import pc, Msun, Myr import numpy as np yt.enable_parallelism() #get command line inputs, syntax is [field] [size] field = sys.argv[1] try : size = float(sys.argv[2]) except (TypeError, IndexError): print("Error, argument syntax is 'plot.py [field] [size]'") quit(0) ds = yt.load("DD0121/output_0121") time = '{:.3f}'.format(round(ds.current_time.in_units('Myr') - 194.608*Myr, 4)) val, loc = ds.find_max('density') plt = yt.SlicePlot(ds, 'z', field, center= loc, width= (size, 'pc')) plt.set_zlim(field, 1e-21, 1e-12) plt.annotate_particles(ds, size*pc, ptype= 8) #produces 1st error #plt.annotate_particles(ds, size*pc, p_size= 2.0, col= 'k', marker= 'o', stride= 1, ptype= 8, minimum_mass= None, alpha= 1.0) #produces 2nd error plt.annotate_text((0.05, 0.05), 't=' + time + 'Myr', coord_system= 'axis') plt.save("test.png") The script seems to run ok until attempting to save the plot, when I get the following error: Traceback (most recent call last): File "plot_yt.py", line 35, in <module> plt.save("test.png") File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_container.py", line 78, in newfunc args[0]._setup_plots() File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 949, in _setup_plots self.run_callbacks() File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1005, in run_callbacks sys.exc_info()[2]) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 999, in run_callbacks callback(cbw) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 53, in _check_geometry return func(self, plot) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 1575, in __call__ reg = self._get_region((x0,x1), (y0,y1), plot.data.axis, data) File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 1639, in _get_region LE[zax] = data.center[zax].ndarray_view() - self.width*0.5 yt.utilities.exceptions.YTPlotCallbackError: annotate_particles callback failed with the following error: unsupported operand type(s) for *: 'EnzoDataset' and 'float' I've tried adding all the keyword arguments and their parameters to the annotate_particles call (switching the commented line on my script), but this produces: Traceback (most recent call last): File "plot_yt.py", line 35, in <module> plt.save("test.png") File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_container.py", line 78, in newfunc args[0]._setup_plots() File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 949, in _setup_plots self.run_callbacks() File "/opt/apps/yt/3.3.1/yt-conda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 997, in run_callbacks callback = CallbackMaker(*args[1:], **kwargs) TypeError: __init__() got multiple values for keyword argument 'p_size' Any help on getting this to work would be vastly appreciated. I was also wondering whether it was possible to use the annotate_particles callback on OffAxisSlicePlots and OffAxisProjectionPlots, I've tried both and neither seems to support this functionality. Many thanks, Sam Patrick

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Question about radial_velocity
by Yuan Li 15 Jun '18

15 Jun '18

Dear yt-users, I was making a plot with "radial_velocity" and noticed that it is always positive, which is odd (there should be both inflow and outflow). The source code is: >>> print(ds.field_info["gas","radial_velocity"].get_source()) def _radial(field, data): return data[ftype, "%s_spherical_radius" % basename] I find that quite confusing. It also looks the same as (‘gas’, ‘radial_magnetic_field’) according to http://yt-project.org/doc/ reference/field_list.html Thank you!

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add_field r/rvir
by Stephanie Tonnesen 14 Jun '18

14 Jun '18

Hi yt-users! I am trying to add a field that is radius/rvir. This is an idealized galaxy sim with static DM potential (no live halo), so I was planning on putting the virial radius in by hand. I am not totally sure what is causing yt to choke--does it not like that I am putting in a number? See below for details. Thanks in advance for any help! Best, Stephanie The lines of code: def rrvir(field,data): return data['radius'].in_units('kpc')/(218.,'kpc') i =0 while i < len(loop): ds = yt.load("blahblah/DD"+loop[i]+"/sb_"+loop[i]) ds.add_field(('gas','r_rvir'),function=rrvir) ....many unimportant lines.... I get this error message: yt : [INFO ] 2018-06-14 09:02:48,783 Gathering a field list (this may take a moment.) yt_slices_allouts_mli.py:19: UserWarning: Because 'sampling_type' not specified, yt will assume a cell 'sampl ing_type' ds.add_field(('gas','r_rvir'),function=rrvir) Traceback (most recent call last): File "yt_slices_allouts_mli.py", line 19, in <module> ds.add_field(('gas','r_rvir'),function=rrvir) File "/home/stonnesen/yt-conda/src/yt-git/yt/data_objects/static_output.py", line 1221, in add_field deps, _ = self.field_info.check_derived_fields([name]) File "/home/stonnesen/yt-conda/src/yt-git/yt/fields/field_info_container.py", line 366, in check_derived_fi elds fd = fi.get_dependencies(ds = self.ds) File "/home/stonnesen/yt-conda/src/yt-git/yt/fields/derived_field.py", line 210, in get_dependencies e[self.name] File "/home/stonnesen/yt-conda/src/yt-git/yt/fields/field_detector.py", line 108, in __missing__ vv = finfo(self) File "/home/stonnesen/yt-conda/src/yt-git/yt/fields/derived_field.py", line 250, in __call__ dd = self._function(self, data) File "yt_slices_allouts_mli.py", line 13, in rrvir return data['radius'].in_units('kpc')/(300.,'kpc') File "/home/stonnesen/yt-conda/src/yt-git/yt/units/yt_array.py", line 1372, in __array_ufunc__ out=out, **kwargs) TypeError: ufunc 'true_divide' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe'' -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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downloading yt using all-in-one script
by Stephanie Tonnesen 11 Jun '18

11 Jun '18

Hi yt-users, I am putting yt on a new machine, and it looks like I will have to use the all-in-one script. I would like to install yt-dev. To do that, what do I need to rename the BRANCH= to? Thanks! Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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Question on Using Parallel Functionality
by Lauren Corlies 11 Jun '18

11 Jun '18

Hi everyone, I'm working on doing an analysis on the ~500 outputs I have from a simulation run so naturally I want to do it in parallel. The data lives on Pleiades where a single node has 32/64 Gb depending on the machine you pick. The general code structure is to take a dataset and compute the fluxes of multiple quantities binned in radius. Because the outputs are large, I'd like to load in 1 dataset per node but then use all 16 cores on the node for the radial flux calculations. To test my code, I'm using 2 smaller outputs of ~4.5 Gb each so they should easily fit on one node but I keep getting memory errors from pleiades. The code does run correctly on my laptop. I'm fairly certain I'm not setting up the code correctly with the different num_proc keywords so that it's trying to do the calculation on a single core instead of half the node. I've posted a paired down example of my code to pastebin that uses two outputs from enzo_comoslogy_plus dataset. The code is named "flux_test_parallel.py" and should run if put inside that dataset directory. The parallel portion of the code is preceded by a line of #'s. ( http://paste.yt-project.org/show/21/) Any advice for how to force the parallel structure to use the machine memory correctly or general pointers for this kind of script would be really appreciated! Thanks! Lauren

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yt-users June 2018