yt-users November 2010

yt-users@python.org

16 participants
19 discussions

Re: [yt-users] calculation of distance in periodic volume
by Stephen Skory 30 Nov '10

30 Nov '10

This is hilarious, because there is also one in yt/utilities/math_utils.py. I wonder which one is better? :) Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice) > >From: Britton Smith <brittonsmith(a)gmail.com> >To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> >Cc: >Sent: Tuesday, November 30, 2010 11:05:47 AM >Subject: Re: [yt-users] calculation of distance in periodic volume > > >Hi Eric, > >I wrote some code to do this for the LightRay tool. In your yt dir, have a look at yt/analysis_modules/light_ray/light_ray.py. Near the bottom, there is a function called periodic_distance. That should have what you need. > >Britton > > >On Tue, Nov 30, 2010 at 12:24 PM, Eric Hallman <hallman13(a)gmail.com> wrote: > >>>Hey, >>>> I am wondering if there is a simple routine in yt for calculating the minimum distance between two points in a periodic volume. Somehow I wind up writing a new routine for this every time I do it, and it requires a bunch of loops to check which distance is right. There is bound to be a faster easier way, wondering if anyone knows of one in yt, or has one they use that works fast. >> >>>>thanks! >> >>>>Eric Hallman >>>>Google Voice: (774) 469-0278 >>hallman13(a)gmail.com >> >> >> >> >>>>_______________________________________________ >>>>yt-users mailing list >>yt-users(a)lists.spacepope.org >>>>http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > >

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calculation of distance in periodic volume
by Eric Hallman 30 Nov '10

30 Nov '10

Hey, I am wondering if there is a simple routine in yt for calculating the minimum distance between two points in a periodic volume. Somehow I wind up writing a new routine for this every time I do it, and it requires a bunch of loops to check which distance is right. There is bound to be a faster easier way, wondering if anyone knows of one in yt, or has one they use that works fast. thanks! Eric Hallman Google Voice: (774) 469-0278 hallman13(a)gmail.com

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YT with RAMSES
by Sam Geen 25 Nov '10

25 Nov '10

Hi, This might be a dumb question, but how do you get YT to work with RAMSES? I tried naively following the guidelines in the Quick Start guide, and it didn't work: --- In [5]: pf = load("../output_00001") yt ERROR 2010-11-25 09:58:43,587 Couldn't figure out output type for ../output_00001 --- I couldn't find anything by searching the online documentation, paper on arXiv or the mailing list archives. Any advice on how to get it working? Thanks, Sam

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parallel config issue
by Sam Skillman 24 Nov '10

24 Nov '10

Hi All, With the new configuration setup, I'm having issues with parallel analysis: simple_proj.py: from yt.mods import * pf = load('DD1701') pc = PlotCollection(pf,center=[0.5]*3) pc.add_projection('Density',0,weight_field='Density') Below is the full error message. I'm not sure if this is due to my implementation somehow or something to do with the config change. Any help would be appreciated. Sam 32Mpc64grid/DD1701:mpirun -np 2 python simple_proj.py --parallel yt DEBUG 2010-11-24 02:24:24,890 Set log level to 0 yt DEBUG 2010-11-24 02:24:24,890 Set log level to 0 yt DEBUG 2010-11-24 02:24:24,944 SIGUSR1 registered for traceback printing yt DEBUG 2010-11-24 02:24:24,945 SIGUSR2 registered for IPython Insertion yt DEBUG 2010-11-24 02:24:24,944 SIGUSR1 registered for traceback printing yt DEBUG 2010-11-24 02:24:24,945 SIGUSR2 registered for IPython Insertion yt INFO 2010-11-24 02:24:26,127 Parallel computation enabled: 0 / 2 yt INFO 2010-11-24 02:24:26,127 Parallel computation enabled: 1 / 2 Traceback (most recent call last): File "simple_proj.py", line 1, in <module> from yt.mods import * File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/mods.py", line 42, in <module> from yt.data_objects.api import \ Traceback (most recent call last): File "simple_proj.py", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/data_objects/api.py", line 34, in <module> from hierarchy import \ from yt.mods import * File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/mods.py", line 42, in <module> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/data_objects/hierarchy.py", line 40, in <module> from yt.data_objects.api import \ from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 52, in <module> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/data_objects/api.py", line 34, in <module> from hierarchy import \ ytcfg["yt","__parallel_rank"] = str(MPI.COMM_WORLD.rank) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/data_objects/hierarchy.py", line 40, in <module> AttributeError: ConfigParser instance has no attribute '__setitem__' from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/yt-2.0dev-py2.6-macosx-10.6-i386.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 52, in <module> ytcfg["yt","__parallel_rank"] = str(MPI.COMM_WORLD.rank) AttributeError: ConfigParser instance has no attribute '__setitem__'

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Camera & HomogenizedVolume
by Stella Offner 24 Nov '10

24 Nov '10

Hi, I updated yt to the new release, and now I'm getting 'NameError: name 'Camera' is not defined' for Camera and HomogenizedVolume (these were both part of the volume_rendering extension previously). Did these get renamed or do I need to import something else? Thanks! Stella

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kd-Tree rendering
by Sam Skillman 24 Nov '10

24 Nov '10

Hi all, I just wanted to announce that the new kd-Tree rendering framework is now in the 'yt' branch of the repository. There are a couple things I wanted to point to if you are interested. The changeset itself: http://yt.enzotools.org/changeset/c7947fef16ac/ A post on blog.enzotools.org highlighting some recent successes: http://blog.enzotools.org/amr-kd-tree-rendering-added-to-yt A simple script, where you should just have to change the parameter file name: http://paste.enzotools.org/show/1367/ A more advanced script that exposes a few new options: http://paste.enzotools.org/show/1368/ Both of these scripts should be able to be run in parallel (as long as N is a power of 2 for now) transparently as: mpirun -np N python script.py --parallel Parallel performance will depend on the structure of your data, but the docs for the Camera object have some suggestions. If you find any problems or have any thoughts, let me know! Best, Sam

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Upgrading the stable version of yt to new module names
by Matthew Turk 19 Nov '10

19 Nov '10

Hi all, I'm writing about upgrading the "stable" version of yt to the a new naming scheme. Before I say anything else, let me start out and say that because of the potentially disruptive nature of this change, you should feel free to either refrain from upgrading your yt installation or emailing me directly (off-list) to get assistance with the upgrade process. We're planning on moving the "stable" version of the code to be the 2.0 API in the next few weeks, where we have removed the names lagos, raven, etc, in favor of more informative names like visualization, data_objects, and so on. This change was described by Jeff in an email to the list a few months ago, which has been summarized here: http://yt.enzotools.org/wiki/yt-2.0 . I would like to encourage you to upgrade now, rather than later, so that we can try to work out any potential issues in advance of the upgrade of the title "stable." Documentation is almost completely update and will be done before the "stable" branch reflects the new API. I've updated the homepage to now encourage new users to use the development version, which features the new module names, etc. If you would like to continue using the version you are on, you should be able to continue to do so by not upgrading. If you would like to upgrade, a new installation may be the easiest way, or otherwise you should be able to get the directory name of the current yt installation from "yt instinfo" and execute: "hg pull ; hg up -C yt ; hg purge ; python2.6 setup.py develop" in that directory. I'm working on updating the documentation to reflect this, but the upshot of all of the API changes is that *everything* that is needed to do all the standard analysis tasks is still available just with the command: from yt.mods import * If you are executing anything that requires directly calling "lagos" or "raven", please contact me directly (off-list) and I will assist you with the upgrade of your scripts. If you think it's a relatively broad concern about module naming and so on, feel free to email the list. Thanks very much, Matt

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Computing fields derived from projected quantities
by Christopher Moody 19 Nov '10

19 Nov '10

Howdy folks, I'd like to calculate the 'lambda' field parameter: <r|v|> / ( r sqrt(v^2+sigma^2) ) (Emsellem et. al. http://arxiv.org/abs/astro-ph/0703531). All of the quantities in question are viewed in projection - as an observer would see. As a result, my lambda field depends on the 'camera location' and requires the projected velocity and dispersion fields, as well as the projected radius, to be computed. Is this possible, or rather, how much elbow grease do I have to put in to calculate this stuff? Thanks, chris

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yt method paper on the arXiv
by Matthew Turk 17 Nov '10

17 Nov '10

Hi all, I just wanted to let you know that we posted a yt method paper on the arXiv today, which may be of some interest. http://arxiv.org/abs/1011.3514 Best, Matt

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Re: [yt-users] Energy Spectrum
by Stephen Skory 12 Nov '10

12 Nov '10

Elizabeth, >There's code to calculate two-point functions (like structure functions and two-point correlation functions). That's almost what you want - you could calculate the 2-point correlation function and do a fourier transform of it with numpy to get the power spectrum of your desired quantity. See: > >http://yt.enzotools.org/doc/extensions/two_point_functions.html Let me add to Brian's response and say that, even as the author of the two-point functions framework, I often get confused on how to use it. It's very flexible and powerful, but not entirely intuitive (which are generally opposing things). I put two examples at the bottom of that page on how to do two-point correlations, where the second one is probably closer to what you want. Let me know if you want help on adapting the example to what you want. Good luck! Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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yt-users November 2010