Mailman 3 June 2011 - yt-users

Oblique slices
by Carolyn Peruta 20 Jun '11

20 Jun '11

Hello YT fans! When I make oblique slices on a warped disk (using the angular momentum vector as a normal), I'm getting some odd step-like features: http://galactica.icer.msu.edu/~cperuta/data/face_CuttingPlane__Density.png Here is the edge-on view: http://galactica.icer.msu.edu/~cperuta/data/edge_CuttingPlane__Density.png Should I be worried about the way this looks or is it an artifact of the oblique slice? Best, Carolyn

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Face-centered variables
by John ZuHone 20 Jun '11

20 Jun '11

Has anyone attempted to use yt for face-centered variables? Best, John Z

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Odd runtime error on Snow Leopard
by John ZuHone 16 Jun '11

16 Jun '11

Hi all, I have a strange runtime error after installing yt-dev on Snow Leopard. Traceback (most recent call last): File "/Users/jzuhone/Source/yt-i386/bin/iyt", line 7, in <module> execfile(__file__) File "/Users/jzuhone/Source/yt-i386/src/yt-hg/scripts/iyt", line 3, in <module> from yt.mods import * File "/Users/jzuhone/Source/yt-i386/src/yt-hg/yt/mods.py", line 96, in <module> from yt.visualization.api import \ File "/Users/jzuhone/Source/yt-i386/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/Users/jzuhone/Source/yt-i386/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/figure.py", line 18, in <module> from axes import Axes, SubplotBase, subplot_class_factory File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/axes.py", line 14, in <module> import matplotlib.axis as maxis File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/axis.py", line 14, in <module> import matplotlib.text as mtext File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/text.py", line 31, in <module> from matplotlib.backend_bases import RendererBase File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 41, in <module> import matplotlib.textpath as textpath File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/textpath.py", line 9, in <module> from matplotlib.mathtext import MathTextParser File "/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/mathtext.py", line 52, in <module> import matplotlib._png as _png ImportError: dlopen(/Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/_png.so, 2): Symbol not found: _png_set_longjmp_fn Referenced from: /Users/jzuhone/Source/yt-i386/lib/python2.7/site-packages/matplotlib/_png.so Expected in: dynamic lookup I have tried the following things: 1) using the libpng (1.4.4) installed via Fink vs. the yt local copy of libpng, making sure that the environment variables were set appropriately 2) setting the environment variables CC and CXX as suggested by the script neither of these things seems to make much of a difference. Best, John ZuHone

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Accessing particle_density in a Castro pure nbody simulation
by Steffen Klemer 15 Jun '11

15 Jun '11

Hey, I'm trying to access die derived field "particle_density" via the following script: from yt.mods import * pf = load('plt00000') my_sphere = pf.h.sphere([0,0,0], 1000.0/pf['kpc']) print my_sphere["particle_density"] Result: http://pastebin.com/Hukh7ahB The data is from a pure nbody Castro run and contains no "Density"-Field in the output. Like this: gurke: ~/castro/runs/test_my_ic > yt stats plt00000 yt : [WARNING ] 2011-06-10 10:29:56,591 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2011-06-10 10:29:56,591 No time units. Setting 1.0 = 1 second. yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: current_time = 0.0 yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_dimensions = [64, 64, 64] yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_right_edge = [ 90. 90. 90.] yt : [INFO ] 2011-06-10 10:29:56,593 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2011-06-10 10:29:56,598 Adding particle_count to list of fields yt : [INFO ] 2011-06-10 10:29:56,598 Adding particle_mass_density to list of fields Warning: invalid value encountered in sqrt Warning: divide by zero encountered in divide Warning: divide by zero encountered in divide Warning: invalid value encountered in sqrt level # grids # cells --------------------------- 0 8 262144 ---------------------------- 8 262144 t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years Smallest Cell: Width: 4.557e-25 mpc Width: 4.557e-22 kpc Width: 4.557e-19 pc Width: 9.402e-14 au Width: 2.022e-11 rsun Width: 8.736e-06 miles Width: 1.562e-02 unitary Width: 1.406e+00 1 Width: 1.406e+00 cm Traceback (most recent call last): File "/home/sklemer/yt/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.1dev', 'console_scripts', 'yt')() File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1061, in run_main sys.exit(YT.main()) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 257, in main return self.cmd(args) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd retval = self.onecmd(argv) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd return self._dispatch_cmd(handler, argv) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd return handler(argv[0], opts, *args) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 224, in arg_iterate func(self, subcmd, opts, arg) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 535, in do_stats v, c = pf.h.find_max("Density") File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 55, in find_max mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 68, in find_max_cell_location source.quantities["MaxLocation"]( field, lazy_reader=True) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 91, in __call__ return self._call_func_lazy(args, kwargs) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 98, in _call_func_lazy rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 603, in _MaxLocation if data[field].size > 0: File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__ data = self.data_source._get_data_from_grid(self.grid, item) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 73, in save_state tr = func(self, grid, field) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2313, in _get_data_from_grid if grid[field].size == 1: # dx, dy, dz, cellvolume File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in __getitem__ self.get_data(key) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 190, in get_data self._generate_field(field) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 135, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 309, in __call__ dd = self._function(self, data) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/frontends/castro/fields.py", line 84, in <lambda> add_field(theirs, function=lambda a, b: b[mine], take_log=True) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in __getitem__ self.get_data(key) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 190, in get_data self._generate_field(field) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 125, in _generate_field self.pf.field_info[field].check_available(self) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 276, in check_available validator(data) File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 374, in __call__ raise NeedsDataField(doesnt_have) yt.data_objects.field_info_container.NeedsDataField: (['density']) Or here like this: In [27]: pf.keys() Out[27]: ['miles', 'rsun', 'mpc', 'cm', 'unitary', '1', 'pc', 'kpc', 'au', '1', 'days', 'years', 'DualEnergyFormalism', 'cosmology_calculator', 'TopGridDimensions', 'CosmologyHubbleConstantNow', 'TopGridRank', 'CosmologyOmegaLambdaNow', 'Time', 'HydroMethod', 'CosmologyOmegaMatterNow', 'EOSType', 'particle_velocity_z', 'particle_position_z', 'particle_position_x', 'particle_position_y', 'particle_mass', 'particle_velocity_x', 'particle_velocity_y'] bye /Steffen PS: Sorry for not using the yt-pastebin script but the lodge_it script seems to not work via the http proxy from my mashine. -- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments

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star_density slices
by Elizabeth Tasker 13 Jun '11

13 Jun '11

Hi, Slices of the star_density field are only showing a tiny patch of the area in the corner, rather than the whole region. My script looks like: pc = PlotCollection(pf, center=[17.,11.5, 16]) p = pc.add_slice("star_density", 2) pc.set_width(10, 'kpc') p.modify["grids"]() Density comes out fine and the grids are drawn in but then only a few of them get stars. Elizabeth

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Google Maps-ify your data
by Matthew Turk 10 Jun '11

10 Jun '11

Hi all, A couple of us have been working on a comprehensive notebook web GUI for yt. It's not ready yet. BUT! In advance of that, we've rolled a portion of that into something called the "mapserver" into the development branch. This is a small, standalone webapp that implements a rendered-on-the-fly google maps interface in yt. To run it, just go into a directory that has some data, and run: yt mapserver DD0054/DD0054 (where "DD0054/DD0054" is the same thing you'd feed to "load" in a script.) You can run with --help to see some options, but what it comes down to is that this will slice, but if you want to project, just do -p like so: yt mapserver -p DD0054/DD0054 This will spawn a webserver on port 8080 which you can then hit in a browser. You'll have to forward an SSH tunnel if you're on a remote machine, but that's just a matter of logging in with "ssh -L 8080:localhost:8080". When you're done, just hit Ctrl-C and it'll quit. Anyway, I think this is pretty cool, and hopefully you will too. If you run into any bugs, report them either with "yt bugreport" or by going to http://hg.enzotools.org/yt/issues/new . -Matt

2 1

Clump finding
by Elizabeth Tasker 09 Jun '11

09 Jun '11

Hi everyone, Thanks for the tips regarding the potential slice on a log-scale; it works great. I've been looking into an alternative way of identifying GMCs in my galaxy disk. Currently, I do this via a density contour, since this roughly equates to how it is done observationally, but I would like to look at gravitationally bound systems as a comparison. The slices I've taken of the potential field suggest many of these will contain several of the clouds I currently define separately. I think the find clumps routine might do what I'd like (which would save me a huge amount of time!) but I am a bit confused as to how to use it. In particular, what is the difference between what the script in the cookbook uses here: http://yt.enzotools.org/doc/cookbook/recipes.html#find-clumps and the derived quantity "_IsBound()"? Does the former use the latter? Is it possible to get a list of cells that comprise each clump such that new properties (mass, angular momentum etc) can be calculated from them? Could someone possible point me to the source code? I couldn't see which routines it was in the yt distribution. Thank you! Elizabeth

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ramses_reader broken on Lens?
by gso＠physics.ucsd.edu 09 Jun '11

09 Jun '11

I was trying to test Lens with a fresh install of the devel YT and some simple projections and I got the following: Traceback (most recent call last): File "moviesDens.py", line 3, in <module> from yt.mods import * File "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/mods.py", line 71, in <module> from yt.frontends.ramses.api import \ File "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/api.py", line 31, in <module> from .data_structures import \ File "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/data_structures.py", line 37, in <module> import _ramses_reader ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/_ramses_reader.so) Is this missing GLIBCXX_3.4.11 YT's problem or should I email the NCCS sys admins? From G.S.

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Log scale
by Elizabeth Tasker 09 Jun '11

09 Jun '11

Hi, I'm doing slices of the potential field: p = pc.add_slice("PotentialField", 2) pc.set_width(10, 'kpc') p.set_zlim(-4500,-2500) p.modify["grids"]() Is there a way to force the scale to the logarithmic like for density slices? thanks, Elizabeth

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Reason
by Christine Simpson 08 Jun '11

08 Jun '11

Hi all, I'm not sure if this is the right list to send this to, but I think a bunch of knowledgeable people read this one, and hopefully one of you can help me. I'm trying to use Reason and I'm kind of confused about the ssh tunneling part. I start up yt serve on a remote machine (ranger) and I'm told to create a ssh tunnel by executing these commands: ~C -L55185:localhost:55185 My local machine doesn't recognize "~C" and I'm not sure what it is either. I tried creating an ssh tunnel with this: ssh tg803911(a)ranger.tacc.utexas.edu -L 55185:localhost:55185 I was then able to successfully open the gui in a browser with the url provided, but I am unable to load data (I can view the help though). In order to do the ssh tunnel properly do I need to install something on my local machine? Christine

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