Mailman 3 July 2012 - yt-users

Specific angular momentum
by Latif 12 Jul '12

12 Jul '12

Hi all, I am trying to compute specific angular momentum using YT. I am getting the following error. It is already in derived fields list but does not work. Am i doing some thing wrong here? Any ideas what is going wrong here? Thanks in advance! Cheers Latif pc.add_profile_sphere(150, "kpc", ["Radiuspc", "SpecificAngularMomentum"], weight="CellMassMsun", accumulation=False, x_bins=64, x_log=True, x_bounds=None,lazy_reader=True, id=None, figure=None, axes=None) # x, y, weight id=None, figure=None, axes=None) # x, y, weight File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 1033, in add_profile_sphere figure=figure, axes=axes) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 943, in add_profile_object profile.add_fields(fields[1], weight=weight, accumulation=accumulation) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 147, in add_fields self._lazy_add_fields(fields, weight, accumulation) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 107, in _lazy_add_fields args=args, check_cut=True) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 56, in save_state tr = func(*args, **kwargs) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 243, in _bin_field source_data = self._get_field(source, field, check_cut) File "/home/astro73/mlatif/YT/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py", line 183, in _get_field data.append(source[field][pointI].ravel().astype('float64')) IndexError: index (3) out of range (0<=index<2) in dimension 0

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clump contour callback
by Elizabeth Tasker 10 Jul '12

10 Jul '12

Hi, Instead of the plot modification mechanism: clumps(self, clumps, plot_args=None) Is it possible to pass an extracted region, not in a clump wrapper? Elizabeth

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Best way to load in halos?
by Matthew Turk 10 Jul '12

10 Jul '12

Hi all, If I have a list of halo locations and radii, what is the best way to load that into yt? Specifically, to get back a set of halo objects? Thanks, Matt

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error info "TypeError: unhashable type: 'list'" with FLASH check point data
by Ji Suoqing 08 Jul '12

08 Jul '12

Hi all, I've always been using YT to analyze FLASH data (plot file and check point file), and it works well. However, recently I have added magnetic field into FLASH, so the check point file contains more index: MAGX, MAGY, MAGZ, MAGP, etc. And if I use YT to deal with check point file, error will occur. Say: >>> pf=load('merger_hdf5_chk_0000') yt : [WARNING ] 2012-07-08 08:30:20,419 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2012-07-08 08:30:20,419 No time units. Setting 1.0 = 1 second. yt : [INFO ] 2012-07-08 08:30:20,419 Parameters: current_time = 0.0 yt : [INFO ] 2012-07-08 08:30:20,419 Parameters: domain_dimensions = [64 64 4] yt : [INFO ] 2012-07-08 08:30:20,419 Parameters: domain_left_edge = [ 0.00000000e+00 -6.55360000e+09 0.00000000e+00] yt : [INFO ] 2012-07-08 08:30:20,420 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] yt : [INFO ] 2012-07-08 08:30:20,420 Parameters: cosmological_simulation = 0.0 yt : [WARNING ] 2012-07-08 08:30:20,420 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2012-07-08 08:30:20,420 No time units. Setting 1.0 = 1 second. >>> for field in pf.h.field_list: print field ... yt : [INFO ] 2012-07-08 08:30:35,531 Adding unknown field dens to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field divb to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field eint to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field ener to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field fspd to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field gamc to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field game to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field gpol to list of fields yt : [INFO ] 2012-07-08 08:30:35,532 Adding unknown field gpot to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field magp to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field magx to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field magy to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field magz to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field pres to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field temp to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field velx to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field vely to list of fields yt : [INFO ] 2012-07-08 08:30:35,533 Adding unknown field velz to list of fields Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 172, in hierarchy self, data_style=self.data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 73, in __init__ AMRHierarchy.__init__(self,pf,data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 83, in __init__ self._setup_unknown_fields() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 146, in _setup_unknown_fields ff = self.parameter_file.field_info.pop(field, None) TypeError: unhashable type: 'list' By the way, YT still works fine with plot file in this case. I sincerely appreciate it if you could provide me with any suggestions on this. Best wishes, Suoqing

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readline installation failing
by Pengfei Chen 07 Jul '12

07 Jul '12

Hi guys, I have installed yt (development version) on my Ubuntu 12.04 LTS. Then I tried to install readline so that I can see the previous commands in iyt. I did "pip install readline" under /yt/bin, but it showed error: ============ Building the readline extension module ============ running install running build running build_ext building 'readline' extension gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_RL_CALLBACK -DHAVE_RL_CATCH_SIGNAL -DHAVE_RL_COMPLETION_APPEND_CHARACTER -DHAVE_RL_COMPLETION_DISPLAY_MATCHES_HOOK -DHAVE_RL_COMPLETION_MATCHES -DHAVE_RL_COMPLETION_SUPPRESS_APPEND -DHAVE_RL_PRE_INPUT_HOOK -I. -I/home/madcpf/Documents/dev_yt/include/python2.7 -c Modules/2.x/readline.c -o build/temp.linux-i686-2.7/Modules/2.x/readline.o -Wno-strict-prototypes as: /home/madcpf/Documents/dev_yt/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.22-system.so) gcc -pthread -shared -L/home/madcpf/Documents/dev_yt/lib/ -L/home/madcpf/Documents/dev_yt/lib64/ -L/home/madcpf/Documents/dev_yt/lib/ -L/home/madcpf/Documents/dev_yt/lib64/ -L/home/madcpf/Documents/dev_yt/lib/ -L/home/madcpf/Documents/dev_yt/lib64/ -L/home/madcpf/Documents/dev_yt/lib/ -L/home/madcpf/Documents/dev_yt/lib64/ build/temp.linux-i686-2.7/Modules/2.x/readline.o readline/libreadline.a readline/libhistory.a -lncurses -o build/lib.linux-i686-2.7/readline.so gcc: error: readline/libreadline.a: No such file or directory gcc: error: readline/libhistory.a: No such file or directory error: command 'gcc' failed with exit status 1 ---------------------------------------- Command /home/madcpf/Documents/dev_yt/bin/python2.7 -c "import setuptools;__file__='/home/madcpf/Documents/dev_yt/bin/build/readline/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --single-version-externally-managed --record /tmp/pip-EMEAm1-record/install-record.txt failed with error code 1 in /home/madcpf/Documents/dev_yt/bin/build/readline Storing complete log in /home/madcpf/.pip/pip.log Then I googled the error "gcc: error: readline/libreadline.a: No such file or directory", but I still can't find a way that works. Any ideas what I should do? Thank you! Pengfei

2 2

scripts from old hub?
by Christine Simpson 06 Jul '12

06 Jul '12

Hi all, Is there a place where the scripts on the old hub migrated to? Thanks Christine

2 2

yt installaton failing
by Agarwal, Shankar 05 Jul '12

05 Jul '12

Hi, While trying to install yt on mac, it quits after a while: Installing BZLIB Installing ZLIB Installing PNG Installing FreeType2 Installing HDF5 Installing SQLite3 Installing Python. This may take a while, but don't worry. YT loves you. Installing Mercurial. Installing mercurial-2.0 (arguments: 'mercurial-2.0') Setting YT_DIR=/Users/hitu/Documents/yt/yt-i386/src/yt-hg/ Installing distribute Installing pip Failure. Check /Users/hitu/Documents/yt/yt-i386/yt_install.log. I checked yt_install.log : from pyexpat import * ImportError: No module named pyexpat Something went wrong during the installation. See the error message above. install_script.sh: line 499: /Users/hitu/Documents/yt/yt-i386/bin/easy_install-2.7: No such file or directory Please let me know how to proceed. Thanks Shankar

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Power Spectrum
by Tyler Berg 05 Jul '12

05 Jul '12

Hi, I am trying to plot a power spectrum from some Enzo data. Trying to figure out how to do this, I stumbled across this post: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2012-March/0024… I followed the instructions here, extracting a covering grid and using numpy.fft. My question now is, how do I create the plot? I've tried using PlotCollection, but I get an 'unhashable type' error when I plug in my Fourier transformed data as one of the inputs to the add_profile_sphere command. So how would I go about plotting this? Is there an alternate way to use PlotCollection, or should I be using something else altogether? Thanks in advance, Tyler Berg

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Re: [yt-users] multiple projections
by Massimo Gaspari 03 Jul '12

03 Jul '12

Thank you for the infos, Matt. It is still not totally clear to me what is the final resolution of the projected map (without doing FRB),in particular when I am using several AMR levels. May you clarify that? Thanks, Max

2 1

Projections and field parameters
by John ZuHone 03 Jul '12

03 Jul '12

Hi all, Does anybody know how exactly projections work with field parameters? Suppose I have a field called "ProjectedVelocity" that takes a field parameter "axis" that chooses between the velocity components depending on the axis of projection. The code goes like this: proj = pf.h.proj(axis, "ProjectedVelocity", weight_field="DensitySquared") proj.set_field_parameter("axis", axis) But it looks like this field is being projected before the field parameter is set. Will I get the correct behavior when I do something later with the proj object, like generate an FRB? Best, John Z

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