Mailman 3 July 2010 - yt-users

yt on Kraken
by Stephen Skory 19 Jul '10

19 Jul '10

Hi all, I have updated the common install of yt on Kraken to the latest trunk (r1797), and I've built Python with SQLite support. Let me know if you run into any problems with the install. /lustre/scratch/proj/yt_common/trunk/ _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Minimum Halo Mass
by Brian Crosby 18 Jul '10

18 Jul '10

Does anyone know of a clever way to plot only halos above a certain minimum mass? I would like to continue finding all the halos located with HaloFinder, but plotting all of them is overwhelming the projections that I've been making. Any structure is essentially invisible, as the image is nearly solid black due to all the plotted halos. If anyone has a tip or trick for this, I would be very grateful. Thanks, Brian

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Temperature Projections
by Brian Crosby 16 Jul '10

16 Jul '10

Hi all, Sorry to keep harassing the list, but I just had a job crash while trying to make some simple temperature projections on Ranger. Before crashing, it successfully created and saved Density and DM Density projections, and the Temperature field is present in the *.cpu files, so that's not the problem. Here's the error: Traceback (most recent call last): File "projections.py", line 31, in <module> p = pt.add_projection("Temperature",2) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/raven/plot_collection.py", line 717, in add _projection **field_parameters) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py", line 1205, in __in it__ self._refresh_data() File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py", line 237, in _refr esh_data self.get_data() File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py", line 1416, in get_ data if self.serialize: self._store_fields(field, self._node_name) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py", line 655, in _stor e_fields passthrough = True) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/ParallelTools.py", line 197, in in_or der f2(*args, **kwargs) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HierarchyType.py", line 210, in _relo ad_data_file self._data_file = h5py.File(self.__data_filename, self._data_mode) File "/share/home/01450/bcrosby/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg /h5py/highlevel.py", line 623, in __init__ self.fid = h5f.open(name, h5f.ACC_RDONLY, fapl=plist) File "/share/home/01450/bcrosby/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg /h5py/_sync.py", line 88, in wrap return func(*args, **kwds) File "h5f.pyx", line 74, in h5py.h5f.open (h5py/h5f.c:1228) h5py._stub.IOError: Truncated file (File interface: File has been truncated) TACC: Cleaning up after job: 1472475 TACC: Done. Thanks, Brian

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Halo Finding Problems
by Brian Crosby 15 Jul '10

15 Jul '10

Hi All, I've been trying to find and plot some halos from an Enzo simulation on Ranger and got this error today: Traceback (most recent call last): File "projections.py", line 4, in <module> halos = HaloFinder(pf, padding=0.03) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HaloFinding.py", line 1786, in __init__ self._join_halolists() File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HaloFinding.py", line 1382, in _join_halolists self._groups.sort(haloCmp) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HaloFinding.py", line 1381, in haloCmp return cmp(h1.center_of_mass()[0],h2.center_of_mass()[0]) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/ParallelTools.py", line 133, in single_proc_results retval = func(self, *args, **kwargs) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HaloFinding.py", line 94, in center_of_mass c_vec = self.maximum_density_location() - na.array([0.5,0.5,0.5]) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/ParallelTools.py", line 130, in single_proc_results return func(self, *args, **kwargs) File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.7-svn/yt/lagos/HaloFinding.py", line 125, in maximum_density_location self._max_dens[self.id][1], KeyError: 604 Does anyone know what's going on here? Thanks, Brian

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Merger Tree
by Brian Crosby 09 Jul '10

09 Jul '10

Hi all, I've been trying to make a merger tree for Enzo simulation, am having some trouble. I think that the problem stems from sqlite3, or my misuse of it, but I'm not certain. I keep getting an error that LD_LIBRARY_PATH is undefined, but I currently have it set to $HOME/yt-x86_64/lib/python2.6/sqlite3/ so that may suggest that sqlite3 is not actually the culprit here. The script and output are both attached, any help or suggestions would be very appreciated. Thanks, Brian Crosby

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Slice issues
by Brian Crosby 07 Jul '10

07 Jul '10

Hi all, I've been trying to make a series of plots from the data dumps of an Enzo simulation, but am encountering problems when yt attempts to make slices. At first I thought it was due to some error in the recursion, but after making a much more direct script, it appears to come up as soon as slices are to be created. For what it's worth, projections are made without any problem, it's the slices that are giving me trouble. The output file is attached. Thanks, Brian

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Non-log scale for colorbars
by Nathan Roth 03 Jul '10

03 Jul '10

Hi, I'd like to be able to set up my color bar so that it chooses the velocity gradient based on a linear, and not a log, scale. One of the reasons I would like to do this is to address the fact that yt plots white space on my slice whenever the field I am plotting is exactly zero. Also, this will help me compare my results to those performed by another code. How can I do this? Thanks, Nathan

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