Mailman 3 May 2014 - yt-users

Spherical coordinates
by Joseph Smidt 15 May '14

15 May '14

Hey everyone, This blog post [1] makes it look like if you have the latest hg tip of yt you might be able to do slices of data in spherical coordinates. Could someone explain how with a simple example since I don't see any documentation? Thanks. [1] http://blog.yt-project.org/post/WhatsUpWith30.html -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

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yt installation issues
by Kaylea Nelson 14 May '14

14 May '14

Hi, I'm trying to install the latest stable yt version via the install_script.sh on a Red Hat 6 based HPC. I'm getting a very confusing error during the final steps of the installation, which can be seen here: http://paste.yt-project.org/show/4612/ Basically, during the step where yt updates from the repo and then attempts to install, it looks in a very odd place for the distribute python package. I can't simply update that version, because I'm on an HPC, but I think the problem is deeper than that. Its looking for it in a version of python that I don't even have loaded in my environment, in a directory that isn't in my PYTHONPATH. I've tried wiping out my python path prior to install as well, but with the same results. From my understanding, yt shouldn't even be trying to use the system version of python any way? Any help would be much appreciated! Kaylea

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RAMSES units bug in yt-3.0
by Sam Geen 13 May '14

13 May '14

Hi, Just to say that in the latest version of yt-3.0 (i.e. since various fields were renamed or re-implemented), I've found a bug in the implementation of "cell_mass", which is giving results that are too low in my runs; I believe the issue is that it's missing a factor of pf["boxlen"]**3 (which is of course only a problem if boxlen is not 1). The previous "CellMass_Msun" worked fine. If I get time I might take a look and issue a pull request, but otherwise I'm just flagging this in case someone else runs into problems; you can just manually multiply the result by pf["boxlen"]**3 until it's fixed. Cheers, Sam

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set_zlim in phase plot
by Chang-Goo Kim 12 May '14

12 May '14

Hi all, set_zlim didn't readjust colormap scale. Here's my simple code and resulting figure. Note that I have tried to reset color scale with set_zlim, but the range remains the same. What did I miss? dd=pf.all_data() ph=PhasePlot(dd,'nH','pok',['cell_mass'],weight_field=None,x_bins=64,y_bins=64,fractional=True) ph.set_zlim('cell_mass',1.e-5,1) ph.show() ph.save('phaseplot.png') http://i.imgur.com/aZ2v7XJ.png BTW, thanks for recent update for fractional keyword. Now, the fractional keyword gives exactly what I want. Chang-Goo

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cylindrical coordinates
by Τρίτσης Άρης- Ευάγγελος 12 May '14

12 May '14

Hi yt users! I am new to yt and would like to ask if anyone has come across issues similar to mine. Is it possible to make slice,projection and 1D-profle plots in cylindrical coordinates in a Flash output file in any orientation and if not does anyone know when such a feature will be implemented to yt? Secondly, when I try to update all dependencies I get the following error: /home/*/yt-x86_64/bin/python2.7: can't open file '/distribute_setup.py': [Errno 2] No such file or directory I would appreciate any help :) Aris

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specify bounds before constructing octree
by Desika Narayanan 12 May '14

12 May '14

Hi Team YT, I have a gadget snapshot that I'd like to specify a sub-region of before constructing an octree, so that the octree built is only over the specified [xmin,xmax], [ymin,ymax],[zmin,zmax] subregion of the original sanpshot? Something just after pf=load(...) presumably is what I want in: http://paste.yt-project.org/show/4606/ though maybe prior to the loading itself? thanks, desika

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Error importing yt.mods
by Sam Geen 09 May '14

09 May '14

Hi, I've downloaded the latest version of the yt-3.0 branch, and have run into some import errors. I've numbered them 1) and 2) below. 1) is "ImportError: No module named owls_subfind.api" and 2) is a problem locating yt.utilities. I've deleted the yt egg file and downloaded a clean cloned version, and the errors persist. Any ideas? Thanks! Sam --- 1) ------ In [1]: import yt.mods yt : [DEBUG ] 2014-05-09 16:07:19,697 Set log level to 0 yt : [DEBUG ] 2014-05-09 16:07:22,067 Registering: Dataset as <class 'yt.data_objects.static_output.Dataset'> yt : [DEBUG ] 2014-05-09 16:07:22,145 Registering: ARTDataset as <class 'yt.frontends.art.data_structures.ARTDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,149 Registering: ARTIODataset as <class 'yt.frontends.artio.data_structures.ARTIODataset'> yt : [DEBUG ] 2014-05-09 16:07:22,152 Registering: AthenaDataset as <class 'yt.frontends.athena.data_structures.AthenaDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: BoxlibDataset as <class 'yt.frontends.boxlib.data_structures.BoxlibDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: OrionDataset as <class 'yt.frontends.boxlib.data_structures.OrionDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: CastroDataset as <class 'yt.frontends.boxlib.data_structures.CastroDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: MaestroDataset as <class 'yt.frontends.boxlib.data_structures.MaestroDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,161 Registering: NyxDataset as <class 'yt.frontends.boxlib.data_structures.NyxDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,165 Registering: ChomboDataset as <class 'yt.frontends.chombo.data_structures.ChomboDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,165 Registering: Orion2Dataset as <class 'yt.frontends.chombo.data_structures.Orion2Dataset'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering: EnzoDataset as <class 'yt.frontends.enzo.data_structures.EnzoDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering: EnzoDatasetInMemory as <class 'yt.frontends.enzo.data_structures.EnzoDatasetInMemory'> yt : [DEBUG ] 2014-05-09 16:07:22,174 Registering simulation: Enzo as <class 'yt.frontends.enzo.simulation_handling.EnzoSimulation'> yt : [DEBUG ] 2014-05-09 16:07:22,178 Registering: FITSDataset as <class 'yt.frontends.fits.data_structures.FITSDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,314 Registering: FLASHDataset as <class 'yt.frontends.flash.data_structures.FLASHDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,317 Registering: GDFDataset as <class 'yt.frontends.gdf.data_structures.GDFDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,321 Registering: HaloCatalogDataset as <class 'yt.frontends.halo_catalogs.halo_catalog.data_structures.HaloCatalogDataset'> yt : [DEBUG ] 2014-05-09 16:07:22,324 Registering: RockstarDataset as <class 'yt.frontends.halo_catalogs.rockstar.data_structures.RockstarDataset'> --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-fcd62da66eec> in <module>() ----> 1 import yt.mods /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/__init__.pyc in <module>() 124 125 from yt.frontends.api import _frontend_container --> 126 frontends = _frontend_container() 127 128 from yt.frontends.stream.api import \ /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/frontends/api.pyc in __init__(self) 39 for frontend in _frontends: 40 _mod = "yt.frontends.%s.api" % frontend ---> 41 setattr(self, frontend, importlib.import_module(_mod)) /home/samgeen/lib/python2.7/importlib/__init__.pyc in import_module(name, package) 35 level += 1 36 name = _resolve_name(name[level:], package, level) ---> 37 __import__(name) 38 return sys.modules[name] /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/frontends/halo_catalogs/api.py in <module>() 25 RockstarFieldInfo 26 ---> 27 from .owls_subfind.api import \ 28 OWLSSubfindDataset, \ 29 IOHandlerOWLSSubfindHDF5, \ ImportError: No module named owls_subfind.api 2) --- In [3]: import yt --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-3-59dfcfe9846c> in <module>() ----> 1 import yt /home/samgeen/.local/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import YTArray, YTQuantity AttributeError: 'module' object has no attribute 'utilities' ----

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Fwd: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy"
by Matthew Turk 08 May '14

08 May '14

---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Thu, May 8, 2014 at 7:45 AM Subject: [astropy-dev] Lorentz Center Workshop on "Python in Astronomy" To: astropy-dev <astropy-dev(a)googlegroups.com>, astropy <astropy(a)scipy.org> Hi everyone, Back in December last year I forwarded a call for proposals for workshops at the Lorentz center to this list, and a few of us subsequently put in an application to hold a Python Astronomy workshop. We are now very happy to report that a "Python in Astronomy" workshop has been accepted and will take place at the Lorentz center in Leiden on 20-24 April 2015. This workshop aims to bring together researchers, Python developers, users, and educators, and will include presentations, tutorials, unconference sessions, and coding sprints. In addition to sharing information about the state-of-the art of Python Astronomy packages, the workshop will also focus on improving interoperability between astronomical Python packages, providing training for new contributors, and developing a common set of educational materials for Python in Astronomy. The meeting is therefore not only aimed at current developers, but also users and educators. A formal website and announcement will come later this year, but we wanted to share this with you now so that you can keep the dates free if you are interested in participating. In the mean time, you can already sign up to receive future announcements about the workshop at the following page: http://python-in-astronomy.github.io Please feel free to spread the word to others that this is happening and get them to sign up to the announcement list. We are very excited about the opportunity to hold this workshop, and we hope to see many of you there! The organizing committee: Thomas Robitaille Pauline Barmby Eric Jeschke Stuart Mumford Magnus Persson -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

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Particle only plots
by Jeremy Ritter 08 May '14

08 May '14

Hello yt, Is there an easy way to plot only particles? What I would like to do is plot a z-axis projection of particle x/y positions, with no background data loaded from the grid. I only see examples for annotate_particles() on top of another plot, but I don't want to unnecessarily load grid data. Thanks! -Jeremy

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Everybody using yt-3.0, turn around
by Matthew Turk 08 May '14

08 May '14

Hi all, Just wanted to drop a note to let you know that we've switched the coordinate system in yt-3.0's mainline to be right-handed. https://bitbucket.org/yt_analysis/yt/pull-request/864/switch-to-right-hande… This should only affect projections and slices along the y axis. According to my understanding of the terms and vocabulary of heraldic coats-of-arms, this makes yt 33% less "sinister." -Matt

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