Mailman 3 June 2011 - yt-users

Oblique slices
by Carolyn Peruta June 20, 2011

June 20, 2011

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

2 3

Face-centered variables
by John ZuHone June 20, 2011

June 20, 2011

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

2 1

Odd runtime error on Snow Leopard
by John ZuHone June 16, 2011

June 16, 2011

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-… [View More]

2 1

Accessing particle_density in a Castro pure nbody simulation
by Steffen Klemer June 15, 2011

June 15, 2011

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 … [View More]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 [View Less]

2 5

star_density slices
by Elizabeth Tasker June 13, 2011

June 13, 2011

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

5 15

Google Maps-ify your data
by Matthew Turk June 10, 2011

June 10, 2011

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 … [View More]

2 1

Clump finding
by Elizabeth Tasker June 9, 2011

June 9, 2011

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. … [View More]

3 2

ramses_reader broken on Lens?
by gso＠physics.ucsd.edu June 9, 2011

June 9, 2011

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 \ … [View More]

2 8

Log scale
by Elizabeth Tasker June 9, 2011

June 9, 2011

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

4 3

Reason
by Christine Simpson June 8, 2011

June 8, 2011

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 … [View More]

3 9