Mailman 3 May 2015 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 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 12 Apr '20

12 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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Profile plot of a 2d projection FRB object
by Ben Thompson 03 Jun '15

03 Jun '15

Hello everyone. I was wondering if anyone has had experience with producing a profile plot from a 2d projection object (FRB object). Essentially, what I am trying to do is plot the stellar surface density of a galaxy as a function of radius. This is achieved by doing the following from a disk YT object called cylinder (in which the origional simulation object is called shot) center = cylinder.get_field_parameter("center") normal = cylinder.get_field_parameter("normal") image_width = (100,"kpc") three_image_width = YTArray((image_width[0], image_width[0], image_width[0]),image_width[1]) left = center - image_width right = center + image_width region = shot.region(center, left, right) proj = yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc") the error arrises here prof = yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None ) where I get the error /gpfs/home/........./profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional) 1304 else: 1305 raise NotImplementedError -> 1306 bin_fields = data_source._determine_fields(bin_fields) 1307 fields = data_source._determine_fields(fields) 1308 if units is not None: AttributeError: 'FixedResolutionBuffer' object has no attribute '_determine_fields' Any ideas how to get around this error? Also some other things to add as a postscript. Since how the projection works, if I provide weights=None as a keyword argument within the ProjectionPlot object, I get a surface density (g/cm^2). But also a "cylindrical_r" in cm^2 as well. I *think* the way to get around this is to do another projection where weights="ones", get the radius values out of that profile.. and then in matplotlib, useing the surface density array from the former profile, and the radius bin array from the latter... Produce a plot of the surface density as a function of radius from those two arrays (I might check by hand afterwards to see if this does the trick). This seems kinda convoluted so I am wondering if there is an easier way than this. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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local install of yt on Blue Waters
by Kenza Arraki 01 Jun '15

01 Jun '15

Hi all, I am trying to locally install yt on Blue Waters. I did a module of swap to PrgEnv-gnu and then bash install_script.sh. Has anyone run into this error before? http://paste.yt-project.org/show/5576/ Thanks, Kenza

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Rendering Volume of FLASH file
by Kilian Gärtner 30 May '15

30 May '15

Hi, I want to render a Volume Plot based on data from a FLASH file, which uses HDF5 file format. I tried the tutorial at http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume… with my file, but I always get this error: yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) This is the complete log: yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: current_time = 1.10472907814e+17 yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: domain_dimensions = [16 16 16] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge = [ -2.20000000e+25 -2.20000000e+25 -2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge = [ 2.20000000e+25 2.20000000e+25 2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2015-05-29 20:51:32,513 Loading field plugins. yt : [INFO ] 2015-05-29 20:51:32,513 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded astro (15 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded cosmology (22 new fields) yt : [WARNING ] 2015-05-29 20:51:32,515 Field ('gas', 'number_density') already exists. To override use force_override=True. yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid (63 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid_vector (95 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded geometric (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded local (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded magnetic_field (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded my_plugins (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded species (121 new fields) yt : [INFO ] 2015-05-29 20:51:42,595 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. Ray casting100% ||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 C:\Anaconda\lib\site-packages\yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) C:\Anaconda\lib\site-packages\yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) The image itself is created, but only black, also the rendering process is instantly finished. I've tried it with the "Enzo_64/DD0043/data0043" file as used for the tutorial, this works with errors. Then I've tried using a given FLASH dataset, the "GalaxyClusterMerger" - same result as my dataset, also the error. I'm using Win 8.1 64-bit Anaconda distribution and yt-project 3.1. Also tried the same thing on Ubuntu 14 with freshly installed yt-project, same error. Is there a solution to create a volume render with FLASH files? Thank you for your attention! Kilian

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is there a limit on image size?
by Dave Semeraro 29 May '15

29 May '15

Helly yt-crowd. I am doing some volume rendering in yt and getting some errors when I try to grow the image size. I am trying to write a png image that is 1024 x 1024. I get the following errors: image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) The largest image I can generate is about 800x 800. It is a nice image too I tell ya. Just wish I could do a bigger one to submit for publication. Attached is the script I am using. Any help would be great. Thanks, Dave Semeraro _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Temperature with Enzo
by David Collins 28 May '15

28 May '15

Hi, Everybody-- I have a dumb question about temperature in enzo. Where is it? I thought I rememberd that being a stock derived field, but I don't see it in the enzo frontends. I can go ahead and make a PR for that if there's not something obvious I'm missing. Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Storing multiple calculations using yt.parallel_objects
by Joshua Wall 27 May '15

27 May '15

Dear users, This there a simple way to store multiple values at each step using parallel_objects? I'm doing: ######################################################## yt.enable_parallelism() num_procs = 4 plot = glob.glob(./plot*) my_storage = {} for sto, p in yt.parallel_objects(plots, num_procs, my_storage): sto.result_id = 'energy' + p sto.resutl = dd["total_energy"] sto.result_id = 'Px' + p sto.result = dd["total_mom_x"] ###################################################### which is just overwriting my energy with the momentum. I also tried to just set to different dictionaries without passing it to yt.parallel_objects as storage, but of course each proc as only a local copy then. Cordially, Josh _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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code units
by David Collins 26 May '15

26 May '15

Hi, Everyone-- I'm trying to get code units from enzo for a cosmology run, but in_units('code_density') seems to do nothing. 'code_mass/code_length**3' seems to work. Is this a bug, or a feature? >>> ad['density'].in_units('code_mass/code_length**3') YTArray([ 0.9970247 , 0.99774731, 0.99854185, ..., 0.99993769, 0.99914176, 0.99841755]) code_mass/code_length**3 >>> ad['density'].in_units('code_density') YTArray([ 1.87321000e-29, 1.87456764e-29, 1.87606042e-29, ..., 1.87868293e-29, 1.87718755e-29, 1.87582689e-29]) code_density Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt-users May 2015