Mailman 3 July 2014 - yt-users

by Melinda Soares-Furtado

I have used yt to determine the flux calculation for a region surrounding a single star with a given mass loss rate. This region is right outside the stellar radius (see attached). Comparing the flux calculation to the known mass loss rate, I see that not all of the mass is accounted for and, what's more, improved refinement of the simulation enhances this percentage, however it is still below 70%. I need to calculate the flux for a region surrounding a large group of stars, so simply increasing the refinement is really not an option. Any suggestions as to how I can use yt for my flux diagnostics in a manner that is more accurate? Best, Melinda

4 years, 10 months

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Unstructured grid yt support‏‏ -question

by Ariadna Murguia

Hi! I wrote a while back asking to visualize a dataset in an unstructured grid with AMR and a vtk output file. I was given a script that could do simple visualizations: http://paste.yt-project.org/show/4879/ . I tried altering it in order to visualize my data but (line 39), the number of elements in my vals array is odd, making the reshape become an error. Is there a way around it? Thank you very much Ariadna Murguia Berthier

4 years, 10 months

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Polar Coordinates Help

by Owen McCrossan

Hello, So I have flash code which generates data into polar coordinates and I need to graph this data in polar coordinates with yt as well, but yt is converting into cartesian coordinates. How can I fix this?

4 years, 10 months

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unitless values in 3.0

by Desika Narayanan

Hi All, Is there a way to drop the units for a value in yt 3.0? For example, in astropy, you can get the raw value of x (without units) by accessing x.value. Thanks, desika

4 years, 10 months

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yt surface triangles in mayavi?

by Michael Zingale

Has anyone tried taking the triangles output from yt's surface function and plot them using Mayavi mlab? The 3d support in matplotlib is a bit limited, so I was hoping to work in mayavi. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

4 years, 10 months

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About using mapserver

by 吳佳鴻

Hi All, I’m new to yt’s mapserver function. I’m trying this feature with a sample FLASH data which I got from data hub on my current yt (2.6 version). However, error message came out like the following. And when I used browser to connect to http://127.0.0.1:8080/, I got nothing. Is there anything that I did it in wrong way? Any suggestion is welcome. Thank you in advance. Many thanks, Jia-Hung Wu =======Error Message============= Bottle server starting up (using RocketServer())... Listening on http://127.0.0.1:8080/ Use Ctrl-C to quit. Rocket.Errors.ThreadPool: [INFO ] 2014-07-24 21:20:52,711 Starting Rocket 1.2.3 Rocket.Errors.ThreadPool: [INFO ] 2014-07-24 21:20:52,718 Listening on sockets: 127.0.0.1:8080 =====================

4 years, 10 months

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problem writing fits image

by Juan Camilo Ibanez Mejia

Dear yt users, I was trying to generate a FITS file from one of my simulations but I obtained an error I do not understand and do not know how to solve. I followed the procedure in: http://yt-project.org/docs/dev-3.0/visualizing/writing_fits_images.html and in the moment I call fib = FITSImageBuffer(cvg, fields=["density"]) I obtain the error: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-87-25a548a040e2> in <module>() ----> 1 fib = FITSImageBuffer(cvg, fields=["density"]) /home/jcibanezm/codes/yt30/yt-x86_64/src/yt-hg/yt/utilities/fits_image.pyc in __init__(self, data, fields, units, center, scale, wcs) 104 mylog.info("Making a FITS image of field %s" % (key)) 105 if first: --> 106 hdu = pyfits.PrimaryHDU(np.array(img_data[key])) 107 first = False 108 else: AttributeError: 'NoneType' object has no attribute 'PrimaryHDU' Any idea how can I solve this ? thanks in advance Juan _____________________________ Juan Camilo Ibañez Mejia PhD candidate in physics Institute für Theoretische Astrophysik Heidelberg University jibanez(a)zah.uni-heidelberg.de<mailto:jibanez@zah.uni-heidelberg.de> Research Scholar Department of Astrophysics American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> _____________________________

4 years, 10 months

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Active Particles

by John Regan

Hi All, I'm having trouble reading Active Particle data from Enzo-3.0 outputs. . . . dd = pf.h.all_data() print dd["RadiationParticle", "particle_position_x"] . . gives File "PrintActiveParticleInfo.py", line 18, in <module> print dd["RadiationParticle", "particle_position_x"] File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 325, in __getitem__ self.get_data(key) File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2627, in get_data if self._generate_field(field): File "/homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 358, in _generate_field raise KeyError(field) KeyError: ('RadiationParticle', 'particle_position_x') >From dumping the hdf5 file the dataset (particle_position_x) exists in the group RadiationParticle. I'm probably missing something simple.... but any hints would be appreciated! Oh I'm using yt-2.7.dev John P.S. Is there documentation on the yt website for reading Enzo-3.0 outputs? (yt-x86_64)[regan@taito-login3 GeneralRoutines]$ yt version yt module located at: /homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-hg The supplemental repositories are located at: /homeappl/home/regan/appl_taito/YT/Dev/yt-x86_64/src/yt-supplemental The current version and changeset for the code is: --- Version = 2.7-dev Changeset = e89295c7393d --- This installation CAN be automatically updated. yt dependencies were last updated on Tue Dec 3 18:24:50 EET 2013 To update all dependencies, run "yt update --all". (yt-x86_64)[regan@taito-login3 GeneralRoutines]$

4 years, 10 months

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doc bug?

by Michael Zingale

Looking at the documentation for the PhasePlot here: http://yt-project.org/docs/dev-3.0/visualizing/plots.html#d-phase-plots both of the examples use "weight_field=None", but I think that for the second case, we really want to omit that argument to get an average. Looking at that plot, if we say that is an average, is seems strange to have an H fraction of 100. Am I missing something? -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

4 years, 10 months

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ortho_ray question

by Michael Zingale

I am trying to use ortho_ray. If I do: c = ds.find_max("temperature") coords = c[1] ray = ds.ortho_ray(0, (coords[1], coords[2])) and then plot ray["density"] vs. ray["x"] , I get a jumbled mess. Printing ray["x"], I see that it is not monotonic -- should I expect it to be? The docs seem to suggest that it would be sorted properly. -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

4 years, 10 months

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yt-users July 2014