Mailman 3 September 2010 - yt-users

halo finding on a volume subset
by Irina Dvorkin 22 Oct '10

22 Oct '10

Dear yt users, Is there a way to run the halo finder on part of the simulation volume? For example, I have a box 256 Mpc on a side but I only want to find halos inside a smaller box, say 20 Mpc on a side. Thanks for your help, Irina

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SphereCallback
by Brian Crosby 23 Sep '10

23 Sep '10

Hello everyone, could someone tell me how to plot a sphere in a color other than black? I've got this much working: p.modify['sphere']((x,y,z), radius, ) to plot a sphere at x, y, z of radius radius, but I cannot seem to succeed in changing the color. Thanks, Brian

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Moving to Mercurial: SVN now deprecated
by Matthew Turk 16 Sep '10

16 Sep '10

Hi everyone, The subversion repository for yt has been frozen, and no further updates will be made to it. We're migrating exclusively to mercurial, which is a different mechanism for source control. (There's a bit more info at this blog post: http://blog.enzotools.org/yt-has-moved-to-mercurial ) I'm pretty excited about this -- it should open up yt as a whole to become more user-friendly in adding contributions. I've added appropriate suggestions to the repository: http://yt.enzotools.org/browser/doc/how_to_develop_yt.txt as well as a list of active branches in the repository: http://yt.enzotools.org/wiki/ExistingBranches The installation scripts have been updated, and I've also changed the landing page and wiki to point to the new installation script. If you would like to move to the hg repository, I recommend either swapping out your existing installation or simply re-installing from scratch. The installation instructions have info on how to get either the stable branch or the unstable branch. http://yt.enzotools.org/wiki/InstallationInstructions NOTE: As per Jeff's email from a couple weeks ago, the unstable branch (named 'yt') has moved away from the old naming convention ('lagos', 'raven', 'fido', etc) and to more descriptive names. Here's his message, for reference: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2010-August/000… . For more information on Mercurial, and what all this means, here are some handy links: http://hginit.com http://mercurial.selenic.com/ http://hgbook.red-bean.com/read/ Please feel free to dig around and submit patches! I'm pretty hopeful that this turnover will make development and contribution of patches much more straightforward and easy. Let me know if you run into any problems. Best wishes, Matt

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yt 2.0 on Kraken
by Stephen Skory 14 Sep '10

14 Sep '10

Hi all, I have just installed and built yt-2.0 on Kraken. The Cray CNL kernel has been upgraded on Kraken which means that the old static-Python build requirements are no longer necessary. This means that it is easier to install yt on Kraken, which would seem to make the common install unneeded. However, one of the requirements for running with shared-Python is that various shared libs need to be copied to lustre because the compute nodes cannot see the home disks. This install of yt is in a non-volatile part of lustre, so you don't have to worry about things being deleted from underneath you as a result of automated purges. To use it is simple, your environment needs to be set like this (depending on your $SHELL): export PYBASE=/lustre/scratch/proj/yt_common/2.0 export PATH=$PYBASE/2.0/bin:$PATH export PYTHONPATH=$PYBASE/lib/python2.6/site-packages export LD_LIBRARY_PATH=$PYBASE/lib:$LD_LIBRARY_PATH when you want to run a batch job, you need to also set this (you should probably make the dot-dir by hand, first): export MPLCONFIGDIR=$TG_CLUSTER_SCRATCH/.matplotlib/ Let me know if you have problems! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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how to call HaloMassFcn
by gso＠physics.ucsd.edu 09 Sep '10

09 Sep '10

I'm getting this error on an old script I used to create the halo mass function on Triton I had on top from yt.analysis_modules.halo_finding.api import HaloMassFcn and got: Traceback (most recent call last): File "parallelHF.py", line 52, in <module> hmf = HaloMassFcn(pf, halo_file=filename[3]+"ParallelHopAnalysis.out", NameError: name 'HaloMassFcn' is not defined I was wondering if this is because yt was updated to 2.0 on triton? in the email there's an example of what to use for HaloFinder from yt.analysis_modules.halo_finding.api import HaloFinder so for HaloMassFcn do I do from yt.analysis_modules.halo_????.api import HaloMassFcn can someone fill in what ???? is, or how I can find that information? Or is the 2.0 manual out that I'm not aware of that has this information already? From G.S.

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Re: [yt-users] projection a rectangular region
by Christine Simpson 07 Sep '10

07 Sep '10

Thanks Matt. This kind of worked. The region I want to project is smaller than the entire simulation domain on the face of the projection. When I made the projection, it left the projected region the same size relative to the entire simulation domain and filled in the parts of the domain not projected with white space. Is there a way I can trim the white space, or rather have add_projection size the projection to fit the plotting space? I've attached an image to show you what I mean. Thanks so much! Christine

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BinnedProfile1D
by Jean-Claude Passy 04 Sep '10

04 Sep '10

Hi all, I need to get radial profiles of my sims - like density as a function or radius. I know how to plot them using the method pc.add_profile_sphere but I now need to print out the values in a txt file. For this reason, I tried to use the class BinnedProfile1D. Below is my script: ################################## file = 'DD0000/CommonEnvelope0021' pf = load(file) r_min = pf.h.get_smallest_dx() r_max = 0.4 sphere = pf.h.sphere([0.5, 0.5, 0.5], r_max) prof1d = L.BinnedProfile1D(sphere, 32, "Radius", r_min, r_max,log_space=False, lazy_reader=True) prof1d.add_fields("Density") prof1d.write_out('test.txt','%0.6e','left') ################################## It run well but returned a density profile equal to 0: ############################## [17:25:54] litai05:$ more test.txt # Radius Density 7.812500e-03 0.000000e+00 2.006836e-02 0.000000e+00 3.232422e-02 0.000000e+00 4.458008e-02 0.000000e+00 5.683594e-02 0.000000e+00 6.909180e-02 0.000000e+00 8.134766e-02 0.000000e+00 9.360352e-02 0.000000e+00 1.058594e-01 0.000000e+00 1.181152e-01 0.000000e+00 1.303711e-01 0.000000e+00 1.426270e-01 0.000000e+00 1.548828e-01 0.000000e+00 1.671387e-01 0.000000e+00 1.793945e-01 0.000000e+00 1.916504e-01 0.000000e+00 2.039063e-01 0.000000e+00 2.161621e-01 0.000000e+00 2.284180e-01 0.000000e+00 2.406738e-01 0.000000e+00 2.529297e-01 0.000000e+00 2.651855e-01 0.000000e+00 2.774414e-01 0.000000e+00 2.896973e-01 0.000000e+00 3.019531e-01 0.000000e+00 3.142090e-01 0.000000e+00 3.264648e-01 0.000000e+00 3.387207e-01 0.000000e+00 3.509766e-01 0.000000e+00 3.632324e-01 0.000000e+00 3.754883e-01 0.000000e+00 3.877441e-01 0.000000e+00 ############################## Could someone tell me what I am doing wrong ? Thanks, JC

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yt doesn't see some libraries
by Irina Dvorkin 04 Sep '10

04 Sep '10

Dear yt users, I have the following problem with my yt installation: when I start ipython or iyt I get the following message: WARNING: Readline services not available on this platform. WARNING: The auto-indent feature requires the readline library and so many useful features (like tab-completion) don't work. I have another Python installation on my machine, and there it all works and does not have this warning. I can bear with the annoying editing, but now I wanted to use the sqlite3 library, and it is the same - it works from the other Python installation, but not from the one within yt. How do I tell the yt installation where to look for these libraries? Thanks for your help, Irina

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