Mailman 3 - yt-users

yt instinfo should now be fixed
by Matthew Turk 26 Oct '10

26 Oct '10

Hi everyone, It turns out there was a bug in the yt autoupdater, which I believe I have now fixed. You can manually update your yt installation by changing to the yt source directory (which "yt instinfo" will provide correctly) and typing: hg pull hg up python2.6 setup.py develop And now, once again, "yt instinfo -u" will update you to the current tip of whatever branch you are on. Sorry about the bug. -Matt

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hierarchy.io.pop, projection
by david collins 25 Oct '10

25 Oct '10

Hi, Everybody! In order to ensure all my units are being done correctly, I have a field 'TE' that forces 'TotalEnergy' to be read off disk, like this: def _TE(field,data): return data.hierarchy.io.pop(data, 'TotalEnergy') lagos.add_field("TE", function=_TE, validators=[lagos.ValidateGridType()]) This lets me circumvent the assumptions that yt makes on a field by that name, specifically unit conversion. However, I can't seem to project it. I get the error, below. Does anyone have any ideas of either different ways to do this, or ways around the projection error? Thanks, d. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "tmp.py", line 9, in <module> mp.plot() File "/home/dccollin/yt/uber.py", line 398, in plot fig = self.add_plots(field,axis,FirstOne) File "/home/dccollin/yt/uber.py", line 676, in add_plots **extra_args) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/raven/plot_collection.py", line 719, in add_projection **field_parameters) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 1205, in __init__ self._refresh_data() File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 237, in _refresh_data self.get_data() File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 1380, in get_data self._get_dependencies(fields), self.hierarchy.io) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/ParallelTools.py", line 1438, in _get_dependencies deps += ensure_list(fi[field].get_dependencies(pf=self.pf).requested) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/field_info_container.py", line 297, in get_dependencies self(e) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/field_info_container.py", line 318, in __call__ dd = self._function(self, data) File "xtra_fields.py", line 161, in _TE dataset = data.hierarchy.io.pop(data, 'TotalEnergy') AttributeError: 'fake_io' object has no attribute 'pop' -- Sent from my Stone Tablet and carried by my Pterodactyl.

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anti-aliasing slices with near-constant fields
by Nathan Roth 25 Oct '10

25 Oct '10

Hello, Could I see an example of the lines of code that would allow me to view a slice with anti-aliasing turned off? In a test problem I am running, some fields values start out with constant values across the simulation box, and when I plot slices they show up garbled. Thanks, Nathan

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ghost zones and non-periodic boundary conditions
by j s oishi 24 Oct '10

24 Oct '10

Hi all, I have a question which is kind of a yt question and kind of an enzo question, so first off, my apologies to the non-enzo users. I have something that quite clearly appears to be a boundary value problem on a non-periodic boundary condition. My first method of attack is to load the (single) root grid data object with its ghost zones: pf = load(data) gz = pf.h.grids[0].retrieve_ghost_zones(2,'y-velocity') However, when I do this on a sample I believe not to have the bug, it appears that yt is loading periodic boundary conditions in the non-periodic direction: the first ghost zone on the lower y boundary is exactly equal to the second-to-top active zone, and the second lower y ghost zone exactly equals the top active zone. More concretely, gz['y-velocity'][:,0,2] always equals gz['y-velocity'][:,-4,2] and gz['y-velocity'][:,1,2] always equals gz['y-velocity'][:,-3,2] This is very clear in the (2D) case at hand, since the velocity field is a large gradient in the y-direction. Is it possible that enzo is not outputting its ghost zones, and yt is simply filling using a periodic method? Or does enzo always output ghost zones, and this is simply a manifestation of my bug? I realize this is not a very clear question, but I'm a bit confused myself. thanks, j

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halo finding on a volume subset
by Irina Dvorkin 22 Oct '10

22 Oct '10

Dear yt users, Is there a way to run the halo finder on part of the simulation volume? For example, I have a box 256 Mpc on a side but I only want to find halos inside a smaller box, say 20 Mpc on a side. Thanks for your help, Irina

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get_multi_plot error
by Christine Simpson 21 Oct '10

21 Oct '10

Hi all, I'm trying to make a multi plot and I'm getting an error that I'm not sure how to fix. I'd appreciate any help you could give. I've pasted the error and script below. I'm not sure I understand what the issue is that it is complaining about. What is engineVals? I used this script with the old version of yt, although I made a few changes to get it to work with the new repository. Here is the error: yt INFO 2010-10-21 13:06:28,094 Getting the binary hierarchy yt INFO 2010-10-21 13:06:28,488 Finished with binary hierarchy reading yt INFO 2010-10-21 13:07:07,696 Max Value is 1.42629e-28 at 0.5039215087890625 0.5306854248046875 0.5584259033203125 in grid EnzoGrid_2576 at level 8 (16, 15, 6) yt INFO 2010-10-21 13:07:07,698 Created plot collection with default plot-center = [0.5039215087890625, 0.5306854248046875, 0.5584259033203125] Traceback (most recent call last): File "multi_plot_25kpc.py", line 14, in <module> fig, axes, colorbars = get_multi_plot( 2, 1, colorbar=orient, bw = 4) File "/share/home/01112/tg803911/yt_new/yt/yt/visualization/plot_collection.py", line 1672, in get_multi_plot fig.set_canvas(be.engineVals["canvas"](fig)) NameError: global name 'be' is not defined Here is the script that produced it: from yt.mods import * from yt.visualization.api import PlotCollection import matplotlib.colorbar as cb fn = "DD0060/output_0060" orient = 'horizontal' pf = load(fn) pc = PlotCollection(pf) fig, axes, colorbars = get_multi_plot( 2, 1, colorbar=orient, bw = 4) #Density p = pc.add_projection("Density",0,figure = fig, axes = axes[0][0], use_colorbar=False) p.set_cmap("bds_highcontrast") p.set_zlim(8*10**(-6),10**(-3)) #Temperature p = pc.add_projection("Temperature", 0, weight_field="Density",figure=fig, axes=axes[0][1], use_colorbar=False) p.set_cmap("hot") p.set_zlim(500,20000) pc.set_width(25.0, 'kpc') for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation=orient) p.colorbar = cbar p._autoset_label() fig.savefig("%s_z_25kpc" % pf)

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add_ray problem
by david collins 21 Oct '10

21 Oct '10

Hi, all-- I'm having trouble with add_ray. I'm trying to do the following, but I get the error that follows the following. I saw that Dr. Tasker recently did a nearly identical thing with more success. I've tried it both on Triton, with the projects install at /projects/lca-group/bla and a trunk install on Kraken. Any thoughts? It works if I use [0.0]*3 and [1.0]*3 as my endpoints. >>> this_ray = pf.h.ray([0.5]*3,[0.5,0.5,1.0],'Density') >>> f='x-velocity' >>> L = plt.plot(this_ray['x'],this_ray[f]) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "tmp.py", line 5, in <module> L = plt.plot(this_ray['x'],this_ray[f]) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in __getitem__ self.get_data(key) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 424, in get_data for grid in self._grids]) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 529, in _get_data_from_grid mask = na.logical_and(self._get_cut_mask(grid), File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 58, in check_cache cm = func(self, grid) File "/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 542, in _get_cut_mask grid.dds, self.center, self.vec) File "RayIntegrators.pyx", line 156, in yt.amr_utils.VoxelTraversal (yt/amr_utils.c:9986) ZeroDivisionError: float division >>> lagos <module 'yt.lagos' from '/projects/lca-group/local-dev/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/__init__.pyc'> -- Sent from my Stone Tablet and carried by my Pterodactyl.

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pc.add_ray
by Elizabeth Tasker 19 Oct '10

19 Oct '10

Hi, I'd like to plot properties along a line through my simulation box, something that wasn't hard to discover how to do in yt (not least because Matt demonstrated it at the meeting in San Diego!): p = pc.add_ray([0.,5.,5.], [10.,5.,5.], "Density") But the plot at the end has an x-axis running from 0 to 1.0, rather than 0. to 10.0. I tried adding: p.set_xlim(0,10.0) but it seemed disinterested. Can I correct this? Elizabeth

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add_profile_sphere
by Elizabeth Tasker 15 Oct '10

15 Oct '10

Hi, Is there an option for a non-log scale on the y-axis for add_profile_sphere? Thanks! Elizabeth

2 1

Volume rendering issues
by Mike Butler 14 Oct '10

14 Oct '10

Hello, I am trying to make a movie of my data using the off-axis projection recipe in the cookbook. The idea of what I am trying to do is make a 3D movie of my data rotating around an axis. The script itself is located at the end of the email. When 'n' is 0, the projection looks normal, but when L should be [0.1,0.5,1.0] and for the following steps, I get images that look like this: http://www.astro.ufl.edu/~butler85/images/frame_0001.png which has what looks like strange bars running across it. Thanks in advance for any help/suggestions. -Mike for n in range(11): ...: pf=load("Cloud_128AMR4StarsFUV_0101") ...: tf=vr.ProjectionTransferFunction() ...: pf.field_info["Density"].take_log=False ...: c = [0.5,0.5,1.0] ...: L=[n*0.1,0.5,1.0] ...: W=0.8 ...: Nvec = 512 ...: vp=pf.h.volume_rendering(L,W,c,Nvec,tf,whole_box=True) ...: vp.ray_cast() ...: image=na.log10(vp.image[:,:,0]) ...: iw.write_image(image,fn % (n))

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