Mailman 3 May 2014 - yt-users

question about transfer function colorbar
by Michael Zingale 23 May '14

23 May '14

I'm trying to show the transfer function on a volume render. Plotting a velocity component, I set the transfer function with 4 Gaussians all with the same width. The range of the transfer function is -1.e7 to 1.e7, but for some reason, when output, the upper label in the colorbar is not 1.e7 but a bit lower (9.92e6). I am not sure where the code is that draws this, and I am confused why it is not setting the tick at 1.e7. It gets the bottom tick right. Here's an image: http://bender.astro.sunysb.edu/random/test_0000.png and the script: http://bender.astro.sunysb.edu/random/vol_rotate.py any pointers are appreciated. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

3 7

physical quantities
by Desika Narayanan 22 May '14

22 May '14

Hi yt, I have a pretty simple question that I ought to know the answer to - how do I extract the actual values in the field_list or derived_field_list of a ds? For example, I have a field: ('PartType0', 'Coordinates'), but printing something like pf[('PartType0','Coordinates')] doesn't return the list of particle type 0 coordinates (or anything for that matter). Do I have to access this through a pf.all_data() command somehow? Thanks -desika

3 2

Plot of domain subset
by Juan Camilo Ibanez Mejia 22 May '14

22 May '14

Hi yt users, I wanted to know if it is possible somehow to make plots (projections and slices) of a subregion of the domain, e.g. I define a sphere like : sph= pf.h.sphere(center=[0,0,0], radius=(100,'pc’)) Now I want to plot the projection of the density of that region in the x axis: slc = SlicePlot(sph, 'x', 'dens') But then I get the following error: AttributeError: 'AMRSphere' object has no attribute 'domain_width' thanks for your help, Juan _____________________________ Juan Camilo Ibañez Mejia Department of Astrophysics American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> _____________________________

2 1

Completely baffled by camera
by Stephanie Tonnesen 22 May '14

22 May '14

Hi all, I am totally baffled by the camera right now. I have a galaxy that is being stripped by an oncoming wind, and I would like to be able to see both the disk and the tail. I am attaching three different ways (out of what think has been a million permutations) I have tried to get a nice volume rendering, and none do a good job. In particular, when I try to choose specific values for tf layers, by adding a single layer I get a TOTALLY different rendering! (v1 and v2). Can anyone explain why I no longer see the disk when I add that extra layer? Also, when I choose to use tf.add_layers, can I get yt to print out where it has put the layers? Thank you! Stephanie

1 0

ARTIO and find_field_value_at_point
by Alexander A. Kaurov 21 May '14

21 May '14

Hi all, I'm trying to access field value in a given point in ARTIO file (sample data file: sizmbhloz-clref04SNth-rs9_a0.9011 ). The function ' find_field_value_at_point ' seems to be not working. May be I'm using it wrong? Here is the code: from yt.mods import * pf=load('test-data/sizmbhloz-clref04SNth-rs9_a0.9011/sizmbhloz-clref04SNth-rs9_a0.9011.art') pf.h. find_field_value_at_point(('artio', 'HVAR_GAS_DENSITY'),[0.1,0.1,0.1]) And the error: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/kaurov/anaconda/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/data_objects/static_output.py", line 84, in __getattr__ raise AttributeError AttributeError Thanks! Sasha

4 8

Memory overloading on time series
by Sam Geen 20 May '14

20 May '14

Hi, The memory usage in yt is filling up the machine for a time series with ~100 outputs. It seems like the data from previous datasets isn't being cleared from memory, despite calling "del pf" and "gc.collect()". I've tried various suggestions made previously in the mailing list to no effect. I'm using the Ramses frontend with the script attached. Any ideas? Thanks, Sam

3 6

log scale image for zero dynamic range
by Chang-Goo Kim 19 May '14

19 May '14

Hi all, When initial condition is uniform, it has zero dynamic range. Although it has no dynamic range, sometimes I need to plot it with log scale colorbar to make a movie with the same colorbar for later times. But, yt forced switch to linear colorbar. How can I make yt not to do that. Thanks, Chang-Goo

2 7

volume rendering in cylindrical coordinates
by j s oishi 16 May '14

16 May '14

Hi all, I just wanted to introduce Yanfei Jiang, a postdoc at the CfA who using Athena to do global radiation MHD simulations of black hole accretion disks. He's really keen to start using yt, but he wants to know what the status of doing volume rendering in cylindrical coordinates. Sam, I know you've been thinking about this. I'm also quite interested in doing volume rendering of cylindrical coordinates! thanks, Jeff

3 4

yt install error on Mac
by Junhwan Choi (최준환) 15 May '14

15 May '14

Hi yt users, Recently, I try to install the yt on my mac desktop that uses OS X 10.8.4. While installing yt, I face on strange error and fail to insall. ........ self._load() File "/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/demandimport.py", line 74, in _load mod = _hgextimport(_import, head, globals, locals, None, level) File "/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/demandimport.py", line 43, in _hgextimport return importfunc(name, globals, *args) ImportError: dlopen(/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/osutil.so, 2): Symbol not found: __cg_png_create_info_struct Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Users/junhwan2/common/lib/libPng.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO /Users/junhwan2/common/bin/python2.7: can't open file '/Users/junhwan2/common/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory As far as I know, yt script needs to make src/yt-hg directory and cp distribute_setup.py. Hence, I can not understand what this error for. Can anyone tell me how it happens and how I can fix it? FYI, I set DEST_DIR="/Users/junhwan2/common" in the script to install yt in my home dir. Thank you in advance, Junhwan Choi

3 5

particle smoothing bug in latest version of yt
by Desika Narayanan 15 May '14

15 May '14

Hi YT, I have a function that loads a pf from a Gadget data set, and then smooths a few physical quantities (gas metallicity; mass; density) onto an octree, and then returns them: http://paste.yt-project.org/show/4624/ in an older version of yt (3.0) that I'm using: 7cf523a36d10 (yt-3.0) this works, no problem. if I run yt-update, to get to: 4d1488b8fa47 this gives the following traceback copied below. Has something important changed that should affect the way I use smoothing functions? -desika File "/Users/desika/Dropbox/powderday/particle_smooth_yt.py", line 41, in yt_smooth saved["metallicity"] = ad["gas", "metallicity"] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 214, in __getitem__ self.get_data(f) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 623, in get_data self._generate_fields(fields_to_generate) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 640, in _generate_fields fd = self._generate_field(field) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 251, in _generate_field tr = self._generate_fluid_field(field) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 271, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/derived_field.py", line 178, in __call__ dd = self._function(self, data) File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/fluid_fields.py", line 153, in _metallicity tr = data[ftype, "metal_density"] / data[ftype, "density"] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 207, in __getitem__ f = self._determine_fields([key])[0] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 455, in _determine_fields finfo = self.pf._get_field_info(ftype, fname) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 487, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas', 'metal_density')' in snapshot_006.

2 3