Mailman 3 October 2010 - yt-users

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

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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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Installing yt-dev
by Elizabeth Harper-Clark 12 Oct '10

12 Oct '10

Dear All, My computer was just updated with hdf5 and python and I hadn't switched over to hg updating yet (bad Libby). Thus I decided to install YT from scratch to cover all of these bases. However I am getting the following error: Renaming /opt/sage/4.4.4/local/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg into /opt/sage/4.4.4/local/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg.OLD.1286903065.35 Traceback (most recent call last): File "setup.py", line 89, in <module> _before_install() File "/mnt/node_scratch/tmp/tmprEd66X/distribute-0.6.10/distribute_setup.py", line 343, in _before_install _fake_setuptools() File "/mnt/node_scratch/tmp/tmprEd66X/distribute-0.6.10/distribute_setup.py", line 409, in _fake_setuptools res = _patch_egg_dir(setuptools_location) File "/mnt/node_scratch/tmp/tmprEd66X/distribute-0.6.10/distribute_setup.py", line 329, in _patch_egg_dir _rename_path(path) File "/mnt/node_scratch/tmp/tmprEd66X/distribute-0.6.10/distribute_setup.py", line 240, in __no_sandbox return function(*args, **kw) File "/mnt/node_scratch/tmp/tmprEd66X/distribute-0.6.10/distribute_setup.py", line 252, in _rename_path os.rename(path, new_name) OSError: [Errno 30] Read-only file system $ ls -l /opt/sage/4.4.4/local/lib/python2.6/ drwxr-xr-x 46 root root 4096 Sep 21 12:14 site-packages What do i need to change to stop this happening? Also yt_install.log says: "If compilation produces errors, or a large number of warnings, please read README.COMPILATION.PROBLEMS" Where is README.COMPILATION.PROBLEMS? Many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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disk_analysis
by Stephen Skory 04 Oct '10

04 Oct '10

Hi all, I can't seem to find the disk_analysis stuff in yt-2, it's not under the amods listings. Was it missed in the conversion, or kept back for some reason? I haven't actually ever used it, but I going to try to, and couldn't find it! http://yt.enzotools.org/doc/api/generated/extension_types/yt.extensions.dis… Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Announcement: Enzo-2.0
by Matthew Turk 01 Oct '10

01 Oct '10

Dear Colleague, Please pass this email along to any researchers that you feel may be interested, and apologies if you receive multiple copies of this message. Announcing the availability of Enzo Version 2.0 =============================================== We are proud to announce the public release of Enzo version 2.0. Enzo is a parallel code for astrophysical and cosmological simulations utilizing adaptive mesh refinement. Enzo 2.0 features many new physics capabilities including ideal MHD, radiation transport (ray tracing and flux limited diffusion), star particle class, metallicity-dependent cooling, and several new hydro solvers. More importantly, we have introduced new software tools to make using and developing Enzo easier. We have adopted distributed version control using Mercurial which supports the growing Enzo developer community. The documentation has been made more accessible and is now distributed with the source code. We have more than doubled the number of test problems and example problems (as well as the number of developers!) In addition, we have added solution testing to the nightly regression tests. Enzo 2.0 is the product of developments made at UC San Diego, Stanford, Columbia, MSU, CU Boulder, CITA, McMaster, SMU, and UC Berkeley. Enzo 2.0 now lives at http://enzo.googlecode.com/ to reflect its multi-institutional provenance. Prospective users are also encouraged to view online lectures from the 2010 Enzo Users' Workshop at http://lca.ucsd.edu/workshops/enzo2010. Enzo development is supported by grants AST-0808184 and OCI-0832662 from the National Science Foundation. THE ENZO DEVELOPMENT TEAM

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