Mailman 3 October 2014 - 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 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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Error in simple volume rendering
by Daniel Fenn 16 Nov '14

16 Nov '14

Hi, I'm trying to do the simple volume rendering from the cookbook. The data is FLASH HDF5 data, and I'm using version 3.0.2 of yt. The script I'm running is here: http://paste.yt-project.org/show/5183/ However, I'm getting the following error: http://paste.yt-project.org/show/5184/ I guess it has something to do with the AMR tree, but unfortunately I don't know a lot about the specifics of that. Could anyone offer any insight into this problem? Thanks, Daniel

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Unable to set log scale in Phase plot.
by Reju Sam John 04 Nov '14

04 Nov '14

Dear all, I am trying to make a phase plot using YT 2.6, with the following line. *plot = PhasePlot(my_sphere, "Density**", "**Temperature* *","CellMassMsun",weight_field=None,x_log=1,y_log=1).save()* but it is giving me the following error. *plot = PhasePlot(my_sphere, "MachNumber", "CRFractionPreCR","CellMassMsun",weight_field=None,x_log=1,y_log=1).save()* *TypeError: __init__() got an unexpected keyword argument 'x_log'* I also tried with x_log=True.Still the same error. What could be the problem? How to make both x and y in log scale? And also I would like to know is it possible to fix x and y range in phase plot? Thank you. -- Reju Sam John

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Fwd: [enzo-dev] A lightcone problem
by Britton Smith 03 Nov '14

03 Nov '14

Hi GB, I am forwarding this over to the yt-users list as this is a yt issue and not an enzo issue. I am unable to reproduce the issue you're seeing when I use the light cone cookbook recipe. I'm guessing that you're running into a corner case with the light cone generator that is specific to your simulation data. Could you send along the light cone solution file? It should be named lightcone.dat. There might be some clues in there. Britton ---------- Forwarded message ---------- From: Gongbo Zhao <gong-bo.zhao(a)port.ac.uk> Date: Thu, Oct 23, 2014 at 11:35 PM Subject: [enzo-dev] A lightcone problem To: brittonsmith(a)gmail.com Cc: "enzo-dev(a)googlegroups.com" <enzo-dev(a)googlegroups.com> Hi Britton, I used the latest yt (version Version = 3.1-dev; Changeset = bf8f9f98b34a (yt) tip) but I am having problems with the lightcone analysis. When I ran it using the following script, > from yt.analysis_modules.cosmological_observation.api import \ > LightCone > > lc = LightCone('Example_Cosmology_Sim.param', > 'Enzo', 0., 0.1) > lc.calculate_light_cone_solution(seed=123456789, filename='lightcone.dat') > field = 'density' > field_of_view = (600.0, "arcmin") > resolution = (60.0, "arcsec") > lc.project_light_cone(field_of_view, resolution, > field, weight_field=None, > save_stack=True, > save_slice_images=True) I got these error messages, > yt : [INFO ] 2014-10-24 04:29:36,439 Parameters: domain_dimensions = [128 128 128] > yt : [INFO ] 2014-10-24 04:29:36,440 Parameters: domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2014-10-24 04:29:36,440 Parameters: domain_right_edge = [ 1. 1. 1.] > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: initial_time = 1.1703706995e+15 s > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: final_time = 4.31424173577e+17 s > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: stop_cycle = 100000 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: cosmological_simulation = 1 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: box_size = 64.0 Mpccm/h > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: omega_lambda = 0.73 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: omega_matter = 0.27 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: hubble_constant = 0.71 > yt : [INFO ] 2014-10-24 04:29:36,441 Parameters: initial_redshift = 60.0 > yt : [INFO ] 2014-10-24 04:29:36,442 Parameters: final_redshift = 0.0 > yt : [INFO ] 2014-10-24 04:29:36,442 Total datasets: 313. > yt : [INFO ] 2014-10-24 04:29:49,842 create_cosmology_splice: Used 5 data dumps to get from z = 0.100000 to 0.000000. > yt : [ERROR ] 2014-10-24 04:29:49,978 Warning: box fraction required to go from z = 0.099445 to 0.077086 is 1.008644 > yt : [ERROR ] 2014-10-24 04:29:49,978 Full box delta z is 0.022168, but it is 0.022359 to the next data dump. > yt : [INFO ] 2014-10-24 04:29:50,042 Saving light cone solution to lightcone.dat. > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: current_time = 272.816550757 > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: domain_dimensions = [128 128 128] > yt : [INFO ] 2014-10-24 04:29:50,217 Parameters: domain_left_edge = [ 0. 0. 0.] > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: domain_right_edge = [ 1. 1. 1.] > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: cosmological_simulation = 1 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: current_redshift = 0.0994652856936 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: omega_lambda = 0.73 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: omega_matter = 0.27 > yt : [INFO ] 2014-10-24 04:29:50,218 Parameters: hubble_constant = 0.71 > yt : [INFO ] 2014-10-24 04:29:50,220 Making projection at z = 0.099445 from DD0272/DD0272. > Parsing Hierarchy 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 > yt : [INFO ] 2014-10-24 04:29:51,714 Gathering a field list (this may take a moment.) > yt : [INFO ] 2014-10-24 04:29:52,622 Loading field plugins. > yt : [INFO ] 2014-10-24 04:29:52,622 Loaded angular_momentum (8 new fields) > yt : [INFO ] 2014-10-24 04:29:52,622 Loaded astro (14 new fields) > yt : [INFO ] 2014-10-24 04:29:52,623 Loaded cosmology (20 new fields) > yt : [INFO ] 2014-10-24 04:29:52,623 Loaded fluid (56 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded fluid_vector (88 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded geometric (102 new fields) > yt : [INFO ] 2014-10-24 04:29:52,624 Loaded local (102 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded magnetic_field (108 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded my_plugins (108 new fields) > yt : [INFO ] 2014-10-24 04:29:52,625 Loaded species (110 new fields) > Traceback (most recent call last): > File "lightcone.py", line 13, in <module> > save_slice_images=True) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 322, in project_light_cone > weight_field=weight_field) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 267, in barrierize > return func(*args, **kwargs) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone_projection.py", line 84, in _light_cone_projection > data_source=cut_region) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 245, in __init__ > self.get_data(field) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 285, in get_data > self._initialize_chunk(chunk, tree) > File "/opt/apps/enzo/new/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 369, in _initialize_chunk > tree.initialize_chunk(i1, i2, ilevel) > File "QuadTree.pyx", line 330, in yt.utilities.lib.QuadTree.QuadTree.initialize_chunk (yt/utilities/lib/QuadTree.c:4710) > ValueError: Buffer has wrong number of dimensions (expected 1, got 2) It seems to be a buffer dimension problem? Thanks, GB -- You received this message because you are subscribed to the Google Groups "enzo-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to enzo-dev+unsubscribe(a)googlegroups.com. To post to this group, send email to enzo-dev(a)googlegroups.com. Visit this group at http://groups.google.com/group/enzo-dev. For more options, visit https://groups.google.com/d/optout.

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create_profile of linear fields
by Douglas Harvey Rudd 31 Oct '14

31 Oct '14

Hi all, Is there a way to specify the log/non-log scaling of a y-axis variable in create_profile or ProfilePlot.from_profiles? I have some profiles that start flat at an initial time and so the velocity_magnitude is everywhere 0. create_profile succeeds, but ProfilePlot.from_profiles generates a Matplotlib error before I have the ability to specify a scaling: sph = ds.sphere(ds.domain_center, ds.domain_width[0]/2) profile = yt.create_profile(sph, "radius", ["density", "temperature", "velocity_magnitude", "dx"], extrema={'radius':(ds.domain_width[0]/ds.num_grid,ds.domain_width[0]/2.)}, n_bins=int(ds.domain_width[0]*2.**(ds.max_level-1)), logs={'radius':False}, units={'radius':'pc'}) plot = yt.ProfilePlot.from_profiles(profile) Relevant part of the dump: /software/python-2.7-2014q3-el6-x86_64/lib/python2.7/site-packages/matplotlib-1.4.0-py2.7-linux-x86_64.egg/matplotlib/ticker.pyc in view_limits(self, vmin, vmax) 1523 if minpos <= 0 or not np.isfinite(minpos): 1524 raise ValueError( -> 1525 "Data has no positive values, and therefore can not be " 1526 "log-scaled.") 1527 Douglas Rudd Scientific Computing Consultant Research Computing Center drudd(a)uchicago.edu

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yt.lagrangian_volume
by Chen Jingjing 29 Oct '14

29 Oct '14

Hi, I am using the code yt.lagrangian_volume to trace the box that contains the dark matter particles at an early stage(higher redshift). But I was quite confused about the output. I am attaching the output file below. (1) I don't know what the values for the box in the new frame mean, i.e. what is the unit of these values? It seems to be the normalized scale because the values are about 1. But it does not seem to be normalized too because there are some values that are larger than 1. Is that due to the periodicity of the box? (2) The bounding box and box in the new frame seems to have the same size. The difference between the two box is just translation. But I was expecting that the box should be expanding/collapsing. (3) The COM (center of mass) in the output is within neither of the box. Does anyone know how to explain the box values in the output file? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709

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Box Containing the Dark Matter Particles
by Chen Jingjing 29 Oct '14

29 Oct '14

Hi, I am using the code yt.lagrangian_volume to trace the box that contains the dark matter particles at an early stage(higher redshift). But I was quite confused about the output. I am attaching the output file below. (1) I don't know what the values for the box in the new frame mean, i.e. what is the unit of these values? It seems to be the normalized scale because the values are about 1. But it does not seem to be normalized too because there are some values that are larger than 1. Is that due to the periodicity of the box? (2) The bounding box and box in the new frame seems to have the same size. The difference between the two box is just translation. But I was expecting that the box should be expanding/collapsing. (3) The COM (center of mass) in the output is within neither of the box. Does anyone know how to explain the box values in the output file? Thanks, Jingjing -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709

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Annotating PhasePlots
by Stefanie Walch 28 Oct '14

28 Oct '14

Dear all, This might be a stupid question but I’m trying for a few hours to add lines to a PhasePlot I have created. Everything I tried so far failed and I was only able to find some instructions using PlotCollection which is outdated. Is there an easy solution? Thanks and kind regards, Stefanie

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