Mailman 3 November 2013 - yt-users

Announcing: yt 2.6
by Kacper Kowalik 23 Nov '13

23 Nov '13

Hi all, We are pleased to announce the release of yt 2.6. This is a major release that includes new features and major updates along with all the bugs identified and fixed since the release of 2.5.5 on August 28. We currently plan for this to be the final major release of the yt 2.X release series, although bug fix releases will continue for the foreseeable future. Please forward this email to other interested parties. Most notable changes include: * Relicensing whole project to BSD 3-clause * Automated absorption line fitting module developed by Hilary Egan * Significant improvement in documentation in a joint effort of the dev team led by Cameron Hummels * Documentation now includes inlined IPython notebooks, thanks to Nathan Goldbaum * RAMSES, ART, Tiger, Maestro and Castro frontends removal as their counterparts in 3.0 branch exceeded them both performance and capability wise. All users of the aforementioned codes are strongly advised to migrate to yt-3.0 * Python stack update, which now features: ipython-1.1.0, hg-2.8, python-2.7.6 numpy-1.7.1 * New ProfilePlot and PhasePlot classes thanks to Britton Smith, Nathan Goldbaum and Matt Turk. Previous mechanisms (i.e. profiles using PlotCollection) are deprecated and will be removed in future versions. * Projections of the Sunyaev-Zeldovich effect using SZpack implemented by John ZuHone * Generating Mock X-ray Photons now possible thanks to John ZuHone * Introduction of Transfer Function Helper by Sam Skillman * Initial support for installing yt with the package management system Conda. * The addition of a frontend for the Pluto code by Andrew Myers * The addition of an OBJ exporter to enable transparent and multi-surface exports of surfaces to Blender and Sketchfab by Jiill Naiman * yt can now export to RADMC3D thanks to Andrew Myers * Considerably (10x+) faster kD-tree building for volume rendering thanks to Sam Skillman * Full integration and demonstration of all available colormaps included in documentation thanks to Cameron Hummels There have also been a number of minor bugs fixed in this release. Some highlights: * Center of the plot in off_axis_projection plots is now calculated correctly, thanks to William Gray * Several enhancements to PlotWindow made by Nathan Goldbaum: - Save accepts paths to directories - Better handling of highly rectangular domains - Axes and colorbars are now toggleable - Nicer output in ipython notebook - eps_writer is now compatible with PlotWindow, thanks to John Wise * yt command line enhancements thanks to Devin Silvia and Matt Turk * Several enhancements to Athena frontend by John ZuHone * Improvements for OSX support (up to Mavericks) * Updates to halo finding routines by Britton Smith We’d also like to recognize the new contributors to the yt 2.x source code and documentation during the yt 2.5 development cycle: * Hilary Egan * John Forbes * William Gray * Stuart Mumford * Jill Naiman * Doug Rudd * Noel Scudder * Elizabeth Tasker If you are using the stable branch of yt from an installation script, you can upgrade using "yt update" or "yt update --all" to upgrade your full dependency stack. If you are using the development branch, you may already have these fixes. A tarball of this release has been uploaded to the Python Package Index (PyPI). Documentation for this release is available at: http://yt-project.org/docs/2.6/ Previous announcements from the 2.5 release cycle can be found at: 2.5.5: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-August/003… 2.5.4: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-July/00371… 2.5.3: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-June/00366… 2.5.2: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003595… 2.5.1: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-March/002988… Thank you very much, Kacper, on behalf of the yt development team

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Athena units
by Stephanie Tonnesen 21 Nov '13

21 Nov '13

Hi Again, Everyone! So I would also like my figures to be in physical units, instead of in my code units. I *think* the Athena frontend doesn't read in what the unit conversions are (and I am not sure how it would do that). Can I just do something simple like: DensityUnits = 3. density_physunits = grid['density'] * DensityUnits Then, of course, I don't know how I would do a SlicePlot, ProjectionPlot or phaseplot in physical units... Any help/advice/direction is appreciated! Thanks, Stephanie

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Getting yt to ignore empty bins in Radial profile
by k.grisdale＠surrey.ac.uk 21 Nov '13

21 Nov '13

Dear yt Users I am plotting some radial profiles from Ramses data. However some of the bins that yt is using are too small for the course grid from the Ramses data and seem to be missing cell centres from the data. Is there anyway I can either change the bin size between certain radii or get yt to ignore data points with values of 0 and just contact the bins with data? Thanks in advance. Kearn PS: The commands that I am using are below in case they are needed: p6 = load("Ramses_sedov_3d/HD_Runs/l9/output_00006/info_00006.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"]) cen = [0, 0, 0] sphere = p6.h.sphere(cen, 0.5/p6['cm']) r_max = sphere['Radius'][sphere['Density'] == sphere['Density'].max()] sphere.set_field_parameter('r_max', r_max) rsh = r_max[0] rad_profile = BinnedProfile1D(sphere, 1500, 'Radius', 0.0, 1.4, log_space=False) rad_profile.add_fields("VelocityMagnitude") rad_profile.add_fields("Density") rad_profile.add_fields("Pressure”)

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Mailing list was down
by Matthew Turk 21 Nov '13

21 Nov '13

Hi all, Looks like the mailing list was down for a while, but is now back up. So, if you sent anything and got weird bounces, feel free to resend. -Matt

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activating yt
by Desika Narayanan 21 Nov '13

21 Nov '13

Hey Team, I'm trying a fresh install of yt on mac os x (mountain lion). I've done this before successfully a few times, so am surprised at my problems. I'm downloading the bleeding edge version. The install script ran fine, but then nothing in the bin directory actually runs. For example: longtrail:~] desika% which pip /Users/desika/yt-3.0/yt-x86_64/bin/pip [longtrail:~] desika% which python /Users/desika/yt-3.0/yt-x86_64/bin/python [longtrail:~] desika% pip install scipy pip: Command not found. So - maybe I should run 'activate', right? So, then I do (I'm in csh): longtrail:~] desika% echo $YT_DST YT_DST: Undefined variable. [longtrail:~] desika% echo $SHELL /bin/csh [longtrail:~] desika% echo $YT_DEST /Users/desika/yt-3.0/yt-x86_64/ [longtrail:~] desika% source $YT_DEST/bin/activate.csh [yt-x86_64] [longtrail:~] desika% [yt-x86_64] [longtrail:~] desika% which pip /Users/desika/yt-3.0/yt-x86_64/bin/pip [yt-x86_64] [longtrail:~] desika% pip install scipy pip: Command not found. [yt-x86_64] [longtrail:~] desika% ipython ipython: Command not found. So then I try doing things manually.... yt-x86_64] [longtrail:~] desika% echo $LD_LIBRARY_PATH /Users/desika/yt-3.0/yt-x86_64/lib: [yt-x86_64] [longtrail:~] desika% echo $PYTHONPATH /Users/desika/python_packages/dn_python_packages:/Users/desika/hyperion-dust-0.1.0/dust_files:/Users/desika/powderday/:/Users/desika/toolbox/python_tools:/Users/desika/yt-3.0/yt-x86_64/bin/:/Users/desika/yt-3.0/yt-x86_64/lib/python2.7/site-packages/ [yt-x86_64] [longtrail:~] desika% [yt-x86_64] [longtrail:~] desika% pip install sicpy pip: Command not found. So now I'm super confused....am I missing something obvious? thanks, desika

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BoxLib 2D Data
by Elizabeth Lovegrove 21 Nov '13

21 Nov '13

Hello all, I'm working with the CASTRO code, which is built on the BoxLib framework, and I'd like to start using yt to visualize my 2D data. I have yt-3.0 running on my machine but the frontend reports that BoxLib 1D and 2D data are not currently supported. Who should I talk to about getting 2D support up and running? Cheers, Elizabeth L.

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3 by 3 multi plot
by Reju Sam John 20 Nov '13

20 Nov '13

Dear All, I am trying to create a 3 by 3 multi plot of densities at different redshifts. But things are failing. But we managed to create a 1 by 3 multi plot with the following code. Can anybody suggest a method to create a 3 by 3 multi plot of density slice. from yt.mods import * import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 1, colorbar='vertical', bw = 4) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" list = [11,13,22] m=0 for kk in list: fn_i=str(kk) fn=file1+fn_i+file2+fn_i # parameter file to load print fn pf = load(fn) # load data pc = PlotCollection(pf, center=[0.5,0.5,0.5]) # defaults to center at most dense point#dd = pf.h.all_data() p = pc.add_slice("Temperature", 1, figure = fig, axes = axes[0][m], use_colorbar=True) p.set_log_field(True) p.modify["contour"]("Density", ncont=9, plot_args = {'colors':'w'},clim=(5e-30,5e-25)) pc.set_width(15, 'mpc') # change width of all plots in pc m=m+1 for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("Temperature_at_rd00_11,13,22" % pf) -- Reju Sam John

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problem using streamlines
by Kathy Eastwood 20 Nov '13

20 Nov '13

Dear yt folk: I am a yt beginner, using Mac OS X 10.7.5. I am not sure which version of yt I am using -- how do I check? -- but I started using it about 5 weeks ago. Here is my problem. I am trying to create some streamlines. I have followed the cookbook example, and it runs, but there is nothing in my plot -- it is empty. I have tried increasing the scale factor, the "length", and the alpha...all to no avail. (I also note that I have NOT been able to get it to work with a data container such as a sphere rather than the entire pf -- does that sound correct?) I am including the bit of code that tries to do the streamlines...any suggestions as to why I cannot see any velocity streamlines? If I do a sliceplot and annotate the velocities with the same dataset, I can see the vectors there with no problem....but I would like to be able to look at the magnetic fields, etc. I would also like to zoom in on a sphere if at all possible... thanks Kathy Eastwood from yt.visualization.api import Streamlines from mpl_toolkits.mplot3d import Axes3D c = np.array([0.5]*3) N = 100 scale = 1.0 pos_dx = np.random.random((N,3))*scale-scale/2. pos = c+pos_dx streamlines = Streamlines(pf,pos,'velx', 'vely', 'velz', length=1.0) streamlines.integrate_through_volume() fig=plt.figure() ax = Axes3D(fig) for stream in streamlines.streamlines: stream = stream[np.all(stream != 0.0, axis=1)] ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1) plt.savefig('streamlines.png') -- Kathy DeGioia Eastwood, Ph.D. Professor of Physics and Astronomy Northern Arizona University Flagstaff, AZ 86011-6010 Ph: 928-523-7159 FX: 928-523-1371 Kathy.Eastwood(a)nau.edu deliveries: 602 S. Humphreys St., Bldg 19 Rm 209

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plotting halos circles on density projection
by Stefano Bovino 19 Nov '13

19 Nov '13

Hi all, I'm trying to plot halos circles on density projection. I would like to select with the circle only the halos on the center of the box where the resolution is good but it seems that my script is doing something different, here the script: pf = load("RD0022/RedshiftOutput0022") halos = HaloFinder(pf) p = ProjectionPlot(pf, "z", "Density", width = (4.0, 'kpc'), center='max') p.annotate_hop_circles(halos,max_number=5) My first question: i) Should the script be able to select the halos according to the txt file I obtain if I run the halo finder separately?! First 5 more massive should match! ii) the problem is that if I select 5 halos they are all outside the box center, I guess because of resolution artifacts. iii) how can I select the halos based on a mass threshold (let's assume 1e6 solar masses)? My aim is to see at two different times where the halos I want to follow are! Thank you in advance Stefano

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cam.rotate
by John Regan 18 Nov '13

18 Nov '13

Hi All, Just a quick question on rotation of the camera object. When I rotate the camera I notice that the center no longer stays at the focus. I'm running a script which zooms and rotates an object in a timeseries fashion. # Code snippet cam = pf.h.camera(c, L, W, (N,N), transfer_function=tf, north_vector=up, no_ghost=True, steady_north=True) #Rotate about the "Lperp" vector theta = rotation*filenum cam.rotate(theta, rot_vector=Lperp) This pretty much works as I want but after a while a get an output like the one attached with the central density no longer at the center. Is there a way to keep the focus at "c". Cheers, John

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