Mailman 3 February 2012 - yt-users

EPS figures in matplotlib (*slightly* off topic)
by John ZuHone 12 Feb '12

12 Feb '12

Hi all, Firstly, I recognize I should probably send this to a matplotlib list so I will do that also. However, I figure this is not a bad place to ask. I'm using matplotlib to write EPS figures, just simply using fig.savefig("test.eps"). However, I'm getting banding effects in the colorbar that I'm not seeing with other formats. I've attached an example. Any suggestions? Best, John Z

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FLASH hydro parameters?
by Nathan Goldbaum 12 Feb '12

12 Feb '12

Hi all, I just noticed that hydro parameters like Gamma and EOSType are not defined for flash parameter files. This makes it impossible to compute the sound speed using the definition in universal_fields.py. I've already modified the FLASH reader to ignore EOSType but I can't figure out how to gracefully figure out what Gamma is. It looks like enzo somehow automatically detects the existence of the Gamma parameter, but I don't see how the enzo reader does this. Can someone point me to the correct place? Thanks, Nathan

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error extracting 2d phase info with user defined field
by Christine Simpson 11 Feb '12

11 Feb '12

Hi all, I'm having trouble with the script pasted here: http://paste.yt-project.org/show/2159/ I am trying to extract a 2d phase profile with a user defined field. I can make the phase plot in a plot collection with this field by using add_phase_sphere, but I want to write the data to a file and I am getting an error with BinnedProfile2D. The error is pasted with the script. It seems that yt accesses all the fields needed to compute the field, but the field is empty somehow? I'm kind of confused; doesn't add_phase_sphere use BinnedProfile2D to do what it does? Christine

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readline and ncurses
by Elizabeth Tasker 08 Feb '12

08 Feb '12

Hi, I'm trying to install readline to work with iyt via: yt/bin/pip install readline But gcc can't find the libncurses library: gcc -pthread -shared -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ build/temp.linux-x86_64-2.7/Modules/2.x/readline.o readline/libreadline.a readline/libhistory.a -lncurses -o build/lib.linux-x86_64-2.7/readline.so /usr/bin/ld: cannot find -lncurses which is totally on this machine: [taskere@iqaluk ~]$ locate libncurses /lib64/libncurses.so.5 /lib64/libncurses.so.5.7 /lib64/libncursesw.so.5 /lib64/libncursesw.so.5.7 /lib64 is in my LD_LIBRARY_PATH, but it looks like gcc doesn't check that. Any ideas? Elizabeth

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Obtaining projection data value
by Jun-Hwan Choi 08 Feb '12

08 Feb '12

Hi all, I wonder whether that I can obtain the value that generate projection plot. I can make a projection image for my disk using add_projection in the plot_collation. I am interested in to get the projected density value and its position (and its pixel size) to perform the FFT analysis in order to find the non-axisymmertic feature such as disk-bar. Is there way to get this values using yt? Thank you in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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YT analysis questions: cylindrical profile and RMS velocity
by Jun-Hwan Choi 06 Feb '12

06 Feb '12

Hi YT users, I have two questions on the YT analysis: First, I would like to make profiles (mass, angular momentum) in the cylindrical coordinate. In other world, the profiles depend on r_xy (x-y is the cylinder plane). I define disk object and compute Profile as follow: > disk = pf.h.disk(center, [0, 0, -1], (100., 'pc'), (1., 'pc')) > profile = BinnedProfile1D(disk, 50, 'Radius', smallest_bin, largest_bin, lazy_reader=True) ,but I find that Radius is for x,y, and z distance. Can I get the cylindrical profile, if I simply make derived field for RadiusXY and replace Radius? And does there any RadiusXY kind of field exist? Second, I would like to compute the RMS velocity in my disk. However, I would like to compute RMS velocity according to local mean velocity (e.g. mean velocity inside 0.1 pc sphere center on a given position), instead of compute according to global mean velocity. Is there a routine (or way) to compute the local mean velocity in YT and compute RMS of it? I found that some papers with Enzo simulation compute the RMS velocity (such as Kitsuk et al 2007 and Wise et al 2008 although I am not sure whether they use YT or not). Thank you in advance, Junhwan Choi -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Install yt on Eureka.alcf.anl.gov
by Min Long 06 Feb '12

06 Feb '12

Dear yter, Is there anyone who once successfully installed "stable" version of yt on Eureka.alcf.anl.gov? I've tried: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh but it got stuck during the installation of Mercurial: Downloading HDF5 Downloading hdf5-1.8.7.tar.gz from yt-project.org Downloading zlib-1.2.3.tar.bz2 from yt-project.org Downloading bzip2-1.0.5.tar.gz from yt-project.org Downloading libpng-1.2.43.tar.gz from yt-project.org Downloading freetype-2.4.4.tar.gz from yt-project.org Downloading sqlite-autoconf-3070500.tar.gz from yt-project.org Downloading Python-2.7.2.tgz from yt-project.org Downloading numpy-1.6.1.tar.gz from yt-project.org Downloading matplotlib-1.1.0.tar.gz from yt-project.org Downloading mercurial-2.0.tar.gz from yt-project.org Downloading ipython-0.10.tar.gz from yt-project.org Downloading h5py-2.0.1.tar.gz from yt-project.org Downloading Cython-0.15.1.tar.gz from yt-project.org Downloading Forthon-0.8.5.tar.gz from yt-project.org Downloading ext-3.3.2.zip from yt-project.org Downloading ext-slate-110328.zip from yt-project.org Downloading PhiloGL-1.4.2.zip from yt-project.org Installing Mercurial. Installing mercurial-2.0 (arguments: 'mercurial-2.0') Failure. Check /home/long/yt/yt-x86_64/yt_install.log. Below I attached the "yt_install.log" and will very appreciate if you have any suggestions. Thanks, Min -- Min Long Flash Center for Computational Science Dept of Astronomy and Astrophysics University of Chicago 5747 S Ellis Ave. Jo 322 Chicago, IL 60637

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Installing on an IBM Power6
by Andrew Davis 02 Feb '12

02 Feb '12

Hi folks, I'm working on installing yt and enzo on a new (to me) cluster, which is an IBM Power6 running AIX. It's having major issues with installing stuff, from basic things like the tar command not having a -z option, to significant issues actually compiling things. I'm still workign through things, but figured I'd ask if anyone has compiled yt and enzo on an AIX machine before? If not, I'll try to submit the final install script that works, along with details of how I've had to modify various makefiles. Thanks, Andrew ************************************************************* ** Dr. Andrew J. Davis adavis(a)mpe.mpg.de ** ** TMoX Research Group ** ** MPE, Garching www.astro.yale.edu/adavis ** *************************************************************

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modify['marker']
by Elizabeth Tasker 01 Feb '12

01 Feb '12

Hi, Would it be possible to add in the option to specify a colour for the 'marker' plot modification mechanism, like that for 'particles'? Currently, yt colours all the markers differently, but if you have a lot of the same type, it would be great to keep them the same. Elizabeth

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yt workshop 2012: A success!
by Matthew Turk 01 Feb '12

01 Feb '12

Hi all, The yt workshop last week in Chicago ( http://yt-project.org/workshop2012/ ) was an enormous success. On behalf of the organizing and technical committees, I'd like to specifically thank the FLASH Center, particularly Don Lamb, Mila Kuntu, Carrie Eder, for their hospitality; the venue was outstanding and their hospitality touching. Additionally, we're very grateful to the Adler Planetarium's Doug Roberts and Mark SubbaRao for hosting us on Wednesday evening -- seeing the planetarium show as well as volume renderings made by yt users up on the dome was so much fun. The yt workshop was supported by NSF Grant 1214147. Thanks to everyone who attended -- your energy and excitement helped make it a success. Thanks also to the organizing and technical committees: Britton Smith, John ZuHone, Brian O'Shea, Jeff Oishi, Stephen Skory, Sam Skillman, and Cameron Hummels. All talks have been recorded, and you can clone a unified repository of talk slides and worked examples: hg clone https://bitbucket.org/yt_analysis/workshop2012/ A few photos have been put up online, too: http://goo.gl/g02uP As I am able to edit and upload talks, they'll appear on the yt youtube channel as well as on the yt homepage: http://www.youtube.com/ytanalysis Thanks again, and wow, what a week! Matt

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