yt-users June 2019

yt-users@python.org

13 participants
12 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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Ytini installation for Houdini on Windows
by uran san 16 Dec '19

16 Dec '19

Hi guys, I am very new to Ytini's mailing list, mailing lists as well as Houdini. So please bear with me while I pick up the etiquette around this medium. With that out of the way here's my first question: After having succeeded installing Ytini for Houdini on a Mac OS X 10.14 I would now like to achieve the same with my Houdini install on a Windows 10 OS. I have tried to somewhat reproduce all steps described here http://www.ytini.com/getstarted.html#collapseTwoOut (Houdini 17.5 Tested on Mac OS X) on my Windows machine but wasn't surprised to learn that of course Houdini could not find the ytini module when I tried to import it in the python shell. Is there somebody, that could point me . in the right direction of how to install Ytini for Houdini on a Windows 10 OS environment? Not afraid of reading so even hints a re more than welcome. Many Thanks in advance Ur4n

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Covering grid dimensions
by andrea.husseiniova＠gmail.com 25 Jun '19

25 Jun '19

I'm working with a dataset from a particle-based simulation with 64^3 particles and am trying to create a covering grid so that I can create a 3D visualization (using volume rendering). I have a problem with the dimensions of that covering grid. A ProjectionPlot from the covering grid dataset only produces a 2x2x2 pixel plot even though the original dataset ProjectionPlot is a 64x64x64 plot. I tried defining the dimensions of the covering grid to be [64,64,64], which results in a 64 pixel wide plot however data is only present in the first 2x2x2 pixels and the rest of the plot is blank. The way I define my covering grid is shown below. Could someone please suggest a solution to this problem? cov_grid = ds.covering_grid(level=0, left_edge=[-1,-1,-1], dims=ds.domain_dimensions, fields=('deposit','PartType1_density')) #alternate version cov_grid = ds.covering_grid(level=32, left_edge=[-1,-1,-1], dims=[64,64,64], fields=('deposit','PartType1_density')) ds_new = cov_grid.save_as_dataset() grid_ds = yt.load(ds_new)

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mass flux of gas in different temperature bins
by Stephanie Tonnesen 21 Jun '19

21 Jun '19

Hi all, I am having some trouble figuring out how to calculate the mass flux as a function of z-position in a wind-tunnel simulation. I am running Enzo with 5 AMR levels. If I trying and make a 1d-profile with create_profile, I would have to make my bin sizes as small as the highest level of refinement, which means I have plenty of z values with zeros. I tried to make a covering_grid, thinking I could just deal with everything as arrays, but as I expected I run out of memory if I make a covering grid of the whole domain at max resolution. When I create a YTdisk region, I get an error when trying to make a covering_grid: AttributeError: 'YTDisk' object has no attribute 'covering_grid' I then tried to use the surface and calculate_flux commands: surf3 = ds.disk([0.5,0.5,0.5],[0., 0., 1.],(30,'kpc'),(100,'kpc')) surfu = ds.surface(surf3,"z",(54,"kpc")) fluxu = surfu.calculate_flux("x-velocity","y-velocity","z-velocity","density") at which point I get this error: ____________________________________________________ Traceback (most recent call last): File "yt_surface_flux.py", line 85, in <module> fluxu = surfu.calculate_flux("x-velocity","y-velocity","z-velocity","density") File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 1269, in calculate_flux field_x, field_y, field_z, fluxing_field) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 1280, in _calculate_flux_in_grid vc_data = grid.get_vertex_centered_data(vc_fields) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/grid_patch.py", line 310, in get_vertex_centered_data cg = self.retrieve_ghost_zones(1, fields, smoothed=smoothed) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/grid_patch.py", line 272, in retrieve_ghost_zones **kwargs) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 927, in __init__ YTCoveringGrid.__init__(self, *args, **kwargs) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 555, in __init__ self.get_data(fields) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 642, in get_data if len(fill) > 0: self._fill_fields(fill) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/construction_data_containers.py", line 1003, in _fill_fields for chunk in ls.data_source.chunks(fields, "io"): File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1263, in chunks self.get_data() # Ensure we have built ourselves File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1306, in get_data self.index._identify_base_chunk(self) File "/mnt/home/stonnesen/yt-conda/yt/yt/geometry/grid_geometry_handler.py", line 289, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1258, in selector self._selector = sclass(self) File "yt/geometry/selection_routines.pyx", line 860, in yt.geometry.selection_routines.RegionSelector.__init__ RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0. Region left edge = -0.0078125 code_length, Region right edge = 1.0078125 code_length Dataset left edge = 0.0 code_length, Dataset right edge = 1.0 code_length This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller regi on that does not border the edge or override the periodicity for this dataset. ___________________________________________ However, my simulated region is 300 kpc across, so I am not at the edge in any axis. I suppose I have 2 questions: can I make a covering_grid of a region of a simulation, or can I have some guidance on making the calculate_flux command work? Thanks in advance!! Best, Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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Binning with create_profile
by Sam Patrick 19 Jun '19

19 Jun '19

Hello, I'm trying to create a radial profile of the gas density using the create_profile function. Even with the extrema explicitly specified the binning does not take these values. I was wondering whether there was a simple way to work around this? My script and output are bellow: ds = yt.load("DD0077/output_0077") val, loc = ds.find_max('density') sp = ds.sphere(loc, (10.0, 'pc')) rp = yt.create_profile(sp, 'radius', ('gas', 'density'), n_bins= 10, extrema= {'radius':((1e-2, 'pc'), (10.0, 'pc'))}, logs= {'radius':True}) rp.x.in_units('pc') >>>YTArray([0.01497631, 0.02988167, 0.05962177, 0.11896107, 0.23735854, 0.47359256, 0.94494138, 1.88540592, 3.76187938, 7.50593617]) pc (where 0.01 and 10 are expected to be the first and last values) Many thanks, Sam Patrick

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Problem with projection / YTQuantity values must be numeric
by José Mauricio Utreras 18 Jun '19

18 Jun '19

Hi all, Recently I have seen this error more often: >> raise RuntimeError("YTQuantity values must be numeric”) I have been able to solve most of the problems which were related with units (some packages behave differently if I do units*array or array*unit). However, I’m getting an error when I’m trying to project a field, and I don’t know how to solve that Code: . . def _Disk_H(field, data): center = data.get_field_parameter('center') z = data["z"] - center[2] return np.abs(z) yt.add_field("Disk_H", function=_Disk_H, units="pc", take_log=False, validators=[ValidateParameter('center')]) . . . disk_dd = dd.cut_region(["obj['Disk_H'].in_units('pc') < 1.0e3"]) proj = ds.proj('density', 2,data_source=disk_dd,weight_field='density’) Saludos! José Utreras Error: proj = ds.proj('density', 2,data_source=disk_dd,weight_field='density') File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 262, in __init__ self.get_data(field) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 336, in get_data self._handle_chunk(chunk, fields, tree) File "/home/jutreras/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__ self.gen.throw(type, value, traceback) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 960, in _field_parameter_state yield File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 330, in get_data [], "io", local_only = True)): File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 508, in parallel_objects for result_id, obj in oiter: File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 800, in chunks yield self File "/home/jutreras/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__ self.gen.throw(type, value, traceback) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1265, in _chunked_read yield File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 800, in chunks yield self File "/home/jutreras/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__ self.gen.throw(type, value, traceback) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1265, in _chunked_read yield File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 799, in chunks self.get_data(fields) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 805, in get_data ind = self._cond_ind File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 837, in _cond_ind np.logical_and(res, ind, ind) File "/home/jutreras/miniconda3/lib/python3.5/contextlib.py", line 77, in __exit__ self.gen.throw(type, value, traceback) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 960, in _field_parameter_state yield File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/data_objects/selection_data_containers.py", line 833, in _cond_ind res = eval(cond) File "<string>", line 1, in <module> File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/units/yt_array.py", line 1094, in __lt__ return super(YTArray, self).__lt__(oth) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/units/yt_array.py", line 1215, in __array_wrap__ any_nonzero = [np.any(oper1), np.any(oper2)] File "/home/jutreras/miniconda3/lib/python3.5/site-packages/numpy/core/fromnumeric.py", line 2164, in any return _wrapreduction(a, np.logical_or, 'any', axis, None, out, keepdims=keepdims) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/numpy/core/fromnumeric.py", line 84, in _wrapreduction return reduction(axis=axis, out=out, **passkwargs) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/numpy/core/_methods.py", line 43, in _any return umr_any(a, axis, dtype, out, keepdims) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/units/yt_array.py", line 1175, in __array_wrap__ return ret[()] File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/units/yt_array.py", line 1165, in __getitem__ return YTQuantity(ret, self.units, bypass_validation=True) File "/home/jutreras/miniconda3/lib/python3.5/site-packages/yt/units/yt_array.py", line 1353, in __new__ raise RuntimeError("YTQuantity values must be numeric") RuntimeError: YTQuantity values must be numeric

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Bin error in phase plot
by Sam Patrick 12 Jun '19

12 Jun '19

Hi all, I'm trying to write a simple piece of code which produces a phase plot of the entire dataset. I'm currently using yt version 3.5.0 and Python version 3.7.1. Essentially what I have is: val, loc = ds.find_max('density') ad = ds.all_data() plot = yt.PhasePlot(ad, "density", "temperature", "cell_mass", weight_field=None) plot.set_unit('cell_mass', 'Msun') filename = "phase_plot_z={:.2f}.png".format(ds.current_redshift) plot.save(filename) However when I try running the code I get the following error: Traceback (most recent call last): File "phase_plot.py", line 14, in <module> plot = yt.PhasePlot(ad, "density", "temperature", "cell_mass", weight_field=None) File "/opt/apps/yt/jan19/lib/python3.7/site-packages/yt/visualization/profile_plotter.py", line 931, in __init__ fractional=fractional) File "/opt/apps/yt/jan19/lib/python3.7/site-packages/yt/data_objects/profiles.py", line 1207, in create_profile obj.add_fields([field for field in fields]) File "/opt/apps/yt/jan19/lib/python3.7/site-packages/yt/data_objects/profiles.py", line 129, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/opt/apps/yt/jan19/lib/python3.7/site-packages/yt/data_objects/profiles.py", line 627, in _bin_chunk bin_ind_y = np.digitize(bf_y, self.y_bins) - 1 ValueError: bins must be monotonically increasing or decreasing I'm not entirely sure what's happening since there's no part of the code which is interfacing with binning directly. Any light shed on this issue would be much appreciated. Many thanks, Sam Patrick

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Help
by Mitali Mitali Damle Damle 11 Jun '19

11 Jun '19

Hello, I have recently subscribed to the yt mailing list. However, I am having problems signing into my account. Below are my account details: E-mail address: damle(a)uni-potsdam.de Username: Mitali I would be very helpful if you could kindly look into this matter. Regards, Mitali Damle, MSc Astrophysics, University of Potsdam

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Halo finder on baryon field
by Sina Hooshangi 10 Jun '19

10 Jun '19

Hello, I have an enzo cosmology simulation which consists only baryonic matter and no dark matter and I'm trying to find halos on this baryonic field. but the HaloCatalog requests particle_mass and probably all other particle fields. is there any way to run HaloCatalog on baryonic fields without defining particle fields? if not, is there any well-defined way to turn gas fields in particle fields in yt? Thanks.

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yt-users June 2019