Mailman 3 September 2011 - yt-users

subregion halo find
by Geoffrey So Sept. 22, 2011

Sept. 22, 2011

Hi Stephen, I'm trying to do halo finding in a subregion of the box, but do the various halo finders know that the boundary conditions are no longer periodic? If periodic BC is on by default, is there a flag to switch off periodicity during the subregion halo find? From G.S.

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Re: [yt-users] yt on Nautilus
by meecegre＠msu.edu Sept. 19, 2011

Sept. 19, 2011

Hi, I had this same problem on Kracken. Matplotlib tries to create a hidden directory in your home directory when it is loaded, but the compute nodes don't have write access to your home directory. Try adding a line to your job script changing MPLCONFIGDIR to the local directory and see if that fixesit. All credit to Britton who explained this to me! -- Greg ------Original Message------ From: Stephen Skory Sender: yt-users-bounces(a)lists.spacepope.org To: Discussion of the yt analysis … [View More]

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yt on Nautilus
by Carolyn Peruta Sept. 19, 2011

Sept. 19, 2011

When I load the yt module on Nautilus and try to use it I get the following error: File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/bin/yt", line 9, in <module> load_entry_point('yt==2.2dev', 'console_scripts', 'yt')() File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg/pkg_resources.py", line 305, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.… [View More]

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Nearest neighbours
by Elizabeth Tasker Sept. 15, 2011

Sept. 15, 2011

Hi, Is there a routine in yt for returning the nearest neighbours to a cell? I was looking at Sam's amr_kdtree and it mentions bricks.... what's a brick? Is a cell a brick? Is a brick a cell? Is that a deep question? If it's horribly complex, I can work on an extracted uniform mesh, I just thought it would be cool not to. Elizabeth

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generic computation of derivatives
by Wolfram Schmidt Sept. 12, 2011

Sept. 12, 2011

Hi everyone, how can I generically define the derivatives of fields in a yt script (or is there already something to do that in yt)? I want to define, say, second-order centered differences of a field without referring to data["particular field"] but with a place holder for just any field (like in a Fortran or C subroutine) so that I can use this single piece of code for several different fields. Thanks, Wolfram

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load error
by Stephen Skory Sept. 9, 2011

Sept. 9, 2011

Hi all, I am getting the error below on an enzo dataset. I am using a completely fresh install of yt using the development branch. I've tried deleting .yt files and clearing out my ~/.yt directory. Nothing works. Does anyone have any ideas? Thanks! Traceback (most recent call last): File "projections.py", line 9, in <module> pf = load("DD%04d/data%04d" % (this,this)) File "/home/stsk4691/yt/src/yt-hg/yt/convenience.py", line 91, in load return output_type_registry[candidates[… [View More]

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Trouble projecting a derived field
by Nathan Goldbaum Sept. 8, 2011

Sept. 8, 2011

Hello all, Right now I'm trying to generate maps of the Toomre Q in an isolated galaxy simulation. To do so, I'm using yt to generate maps of the gas column density as well as density-weighted projections of the sound speed and orbital frequency, which I'm using as a proxy for the epicyclic frequency. Unfortunately, I'm having some trouble making projected maps of the orbital frequency. I've defined two new derived fields, CylinderRadius and AngularVelocity (http://paste.yt-project.org/show/… [View More]

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combining data objects
by Christine Simpson Sept. 6, 2011

Sept. 6, 2011

Hi all, Is there a simple way I can combine two data objects to create a new data object? For example, if I created two sphere objects, is there a way I can combine them to create an object that contains the data of both of them? Thanks Christine

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setting limits on phase plots
by Christine Simpson Sept. 2, 2011

Sept. 2, 2011

Hi all, I'm trying to make some phase plots and specify the x axis limits, the y axis limits and the color bar limits. I've tried this: pc.add_phase_sphere(r200[j],'kpc',["Density","Temperature","CellMassMsun"],weight=None) pc.set_zlim(1.0**-2,1.0**5) pc.set_xlim(1.0**-30,5.0**-19) pc.set_ylim(10.0,1.0**7) It sets the limits to some random values and I get an empty plot. I thought there was some 'redraw' callback that I could try and I tried 'pc.redraw()' and 'pc.redraw_image()', but I … [View More]

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yt-2.2 Release Announcement
by Cameron Hummels Sept. 2, 2011

Sept. 2, 2011

Release Announcement (Please feel encouraged to forward this message to any other interested parties.) We are proud to announce the release of yt version 2.2. This release includes several new features, bug fixes, and numerous improvements to the code base and documentation. At the new yt homepage, http://yt-project.org/, an installation script, a cookbook, documentation and a guide to getting involved can be found. We are particularly proud of the new GUI, entitled "Reason," which … [View More]allows real-time exploration of datasets, and which can be used (locally or remotely over SSH) with no dependencies other than a web browser. A basic demonstration of its usage can be found at yt is a community-developed analysis and visualization toolkit for astrophysical simulation data. yt provides full support for Enzo, Orion, Nyx, and FLASH codes, with preliminary support for the RAMSES, ART, and Maestro codes. It can be used to create many common types of data products such as: * Slices * Projections * Profiles * Arbitrary Data Selection * Cosmological Analysis * Halo finding * Parallel AMR Volume Rendering * Gravitationally Bound Objects Analysis There are a few major additions since yt-2.1 (Released April 8, 2011), including: * New web GUI "Reason," designed for efficient remote usage over SSH tunnels * Command-line submission to the yt Hub (http://hub.yt-project.org/) <about:blank> * Absorption line spectrum generator for cosmological simulations * Support for the Nyx code * An order of magnitude speed improvement in the RAMSES support * Experimental interoperability with ParaView * Quad-tree projections, speeding up the process of projecting by up to an order of magnitude and providing better load balancing * "mapserver" for in-browser, Google Maps-style slice and projection visualization * Many bug fixes and performance improvements With this release, we also unveil the yt Hub, an astrophysical simulation-specific location for sharing scripts, analysis and visualization tools, documents and repositories used to generated publications. The yt Hub has been designed to allow programmatic access from the command line, and we encourage you to browse the current offerings and contribute your own. The yt Hub can be found at http://hub.yt-project.org/. Documentation: http://yt-project.org/doc/ Installation:http://yt-project.org/doc/advanced/installing.html Cookbook: http://yt-project.org/doc/cookbook/recipes.html Get Involved:http://yt-project.org/doc/advanced/developing.html If you can't wait to get started, install with: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh <http://install_script.sh/> Development has been sponsored by the NSF, DOE, and University funding. We invite you to get involved with developing and using yt! Please forward this announcement to interested parties. Sincerely, The yt development team [View Less]

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