Mailman 3 July 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 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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EnzoDatasetInMemory not working in parallel
by Britton Smith 24 Feb '16

24 Feb '16

Hi all, I've recently been trying to use yt's inline analysis functionality with Enzo and am having some difficultly getting it to work in parallel. I am using the development tip of yt. In serial, everything works fine, but in parallel, I get the following error: http://paste.yt-project.org/show/5694/ It seems that the issue is that yt is not correctly identifying which grids are available on a given processory for the EnzoDatasetInMemory object. Does anyone have an idea of how to fix this? Has anyone else seen this? For reference, my user_script is just this: import yt from yt.frontends.enzo.api import EnzoDatasetInMemory def main(): ds = EnzoDatasetInMemory() ad = ds.all_data() print ad.quantities.total_quantity("cell_mass") Thanks for any help, Britton

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convert arbitrary particle based quantities to cloud-in-cell mesh
by Brendan Griffen 19 Aug '15

19 Aug '15

Hi, I'm looking to convert particle based quantities into a uniform grid based quantity (arepo data is input). So say I have a collection of gas elements with some density rho and x,y,z positions. I want to construct an 256^3 mesh representing the cells in a mesh. x,y,z,rho --> cic mesh where the values at i,j,k is the smoothed density are created by the cic algorithm Now, generalising this more, can I have rho to be any quantity? So now say I have star particles which similarly have x,y,z but I want to distribute their luminosity. Again, I want to do it for say the gas velocity field as well. Is there any general functionality for converting particle quantities to mesh quantites in yt with the deposit all_cic functionality? I have a basic code for just x,y,z particle data and distributing that based on density to a cic (see below) ad = pf.all_data() level = int(math.log(ndim,2)) cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim]) arr = cg['deposit', 'all_cic'], but I'm not sure what to do for the other variables. Any help is appreciated in advance. Thanks. Brendan

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Custom Colorbar Axis
by Gabriel Goodwin 05 Aug '15

05 Aug '15

Hello All, Does anyone know how to specify the tickmark locations on the colorbar axis? I am able to do this on the plot axes without issue, but have not been able to successfully do the same with the colorbar. Attached is a pic of one of my plots using default colorbar axis ticks. I have tried to use the following code (and many variants of it I have found in the python/matplotlib documentation) to specify the location of the tickmarks, but they don't place the ticks accurately. My data is temperature plotted over the range of 300K to 5500K and I want to have tickmarks at 300K, 800K, 3500K, and 4500K. Also attached is pic of my plot showing an attempted custom colorbar axis. I'm not sure if it makes a difference, but I made the colormap in matplotlib. colorbar_axes = p.plots[string].cax colorbar_axes.yaxis.set_ticks([0, 0.1, 0.8]) Thanks for the help!

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Re: [yt-users] Streamlines for FLASH in yt
by Mikhail Klassen 31 Jul '15

31 Jul '15

Hi Michael, John, Nathan, My strealines script can be see here: http://paste.yt-project.org/show/5767/ Modifying the periodicity manually via ds.periodicity = (True, True, True) causes the script to appear to execute for a very long time. I have never seen it run to completion, even for a single streamline. Perhaps I am just impatient. If I do not directly modify the periodicity, the output I have pasted here: http://paste.yt-project.org/show/5768/ Any help is appreciated. Best, Mikhail

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plotting questions
by Shankar Agarwal 31 Jul '15

31 Jul '15

Hi, I have a few plotting questions: 1. http://yt-project.org/docs/3.2/cookbook/simple_plots.html#simple-particle-p… p.set_unit('particle_mass', 'Msun') In the above plot, Colorbar range is approximately Mass=10^5-10^9. When making a plot using ParticlePlot or ParticleProjectionPlot, can I manually force the range on the colorbar? 2. The label on the colorbar says "Particle Mass". Instead, shouldn't it be saying something like mass_per_pixel, since the plot is showing the total number of particles projected along the z-axis? How can we rename the colorbar? 3. Can contours of mass be added to the above plot, using annotate? Regards, Shankar

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Streamlines for FLASH in yt
by Mikhail Klassen 31 Jul '15

31 Jul '15

I'm trying to plot 3D streamlines from a FLASH (v.4) dataset. I've based my streamlines script off the version presented on the yt-project.org website. I consistently get an error about going up the ghost cells in my volume. The error message is: RuntimeError: Error: yt attempted to read outside the boundaries of a > non-periodic domain along dimension 0. > Region left edge = -3e+18 code_length, Region right edge = 4.5e+18 > code_length > Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19 > code_length > This commonly happens when trying to compute ghost cells up to the domain > boundary. Two possible solutions are to load a smaller region that does not > border the edge or override the periodicity for this dataset. My FLASH datasets have x/y/zmin = 0.0 and x/y/zmax 1.2e19 cm. I seems like yt is trying to read outside my domain, or is bumping up against the guardcells and I have no idea how to prevent it from doing this. I have tried inspecting the code for an obvious solution. A very similar error shows up when I try to make 1D profiles of the entire dataset (dd = ds.all_data()). is it possible that yt doesn't support volumes where the (0,0,0) coordinate is a corner of the volume? Any easy solution to the above issue? Thanks, Mikhail

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installation_problem
by alex volioths 30 Jul '15

30 Jul '15

Hello everyone, I have just learned about yt and I'd like to try it out. I tried to install it using the shell script but i got the following error:I am using Ubuntu 14.04 64 bit. Installing pip******************************************** FAILURE REPORT:******************************************** bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmp4MGuKb/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module>ImportError: cannot import name HTTPSHandler I have also attached the last lines from the log file. Does anyone knows how can this error be fixed? Thank youAlex

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