Mailman 3 January 2011 - yt-users

CICDeposit_3
by John ZuHone Jan. 20, 2011

Jan. 20, 2011

Hello all, It appears from a cursory look at the source code that CICDeposit_3 does not automatically convert the mapped "mass" to a density itself... that the volume must be divided by after the fact. Is this correct? Best, John Z

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Dumb install question
by david collins Jan. 20, 2011

Jan. 20, 2011

Hi there-- I have a (probably dumb) compilation problem, osx 10.6.2. The end of the yt_install.log is below. I don't quite follow which directory is failing to find setup.py in. Thanks, d. byte-compiling /Users/dcollins/local/lib/python2.6/site-packages/Forthon/compilers.py to compilers.pyc byte-compiling /Users/dcollins/local/lib/python2.6/site-packages/Forthon/Forthon_builder.py to Forthon_builder.pyc byte-compiling /Users/dcollins/local/lib/python2.6/site-packages/Forthon/… [View More]

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Installing Enzo from Yt, error!
by Hector Aceves Jan. 19, 2011

Jan. 19, 2011

Hi to all.. I am new in this Enzo-Yt world, and taking advantage of this mailing list, I will appreciate any help you might give me in installing Enzo and Yt. My problem is as follows. Firstly, I am using the install_script.sh provided by Yt, in a AMD multicore 64 bit computer, with shared memory, gfortran as fortran compiler and also gcc; all this under ubuntu linux. I activated the following options in the script: NUMPY_ARGS="--fcompiler=gnu95" HDF5_DIR= INST_ZLIB = 1 ...… [View More]

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_pdensity_pyx method not defined in yt 2.0
by Chris Malone Jan. 18, 2011

Jan. 18, 2011

Hi, I just performed a clean install of yt 2.0, and upon importing from yt.mods I get a complaint about the undefined field function _pdensity_pyx in yt.data_objects.universal_fields. In particular, it looks like some spurious code has been left around at line 807 of universal_fields.py add_field("particle_density", function=_pdensity_pyx, validators=[ValidateSpatial(0)], convert_function=_convertDensity, display_name=r"\mathrm{Particle}\/\mathrm{Density})") Indeed, … [View More]

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yt-2.0 Release Announcement
by j s oishi Jan. 17, 2011

Jan. 17, 2011

Hi All, We're proud to announce the release of yt version 2.0, an analysis and visualization toolkit for Adaptive Mesh Refinement data. This release features a complete reorganization of the yt internal codebase, a number of bug fixes, and numerous improvements to the code base and the documentation. This is also the first release since the publication of the yt method paper in ApJS (http://adsabs.harvard.edu/abs/2011ApJS..192....9T). The major changes in 2.0 since version 1.7 (Released on … [View More]June 27, 2010) include: * Major reorganization of the codebase for speed, ease of modification, and maintainability * Re-organization of documentation and addition of Orientation Session * Support for FLASH code * Preliminary support for MAESTRO, CASTRO, ART, and RAMSES (contributions welcome!) * Perspective projection for volume rendering * Exporting to Sunrise * Preliminary particle rendering in volume rendering visualization * Drastically improved parallel volume rendering, via kD-tree decomposition * Simple merger tree calculation for FOF catalogs * New and greatly expanded documentation, with a "source" button in the API documentation (see http://yt.enzotools.org/doc/reference/api/generated/yt.data_objects.data_co… for an example) yt features native support for astrophysical data generated by several codes, providing a natural and intuitive way to address physical regions in space as well as processed data. Development has been sponsored by NSF, DoE, and University funding. If you are running an older version of yt, re-obtaining and re-running the installation script should happily upgrade your installation. If you are using an older version that is checked out from the mercurial repository, executing "yt instinfo -u" should also perform the upgrade appropriately. If you are still using an older version obtained from the old (discontinued) SVN repository, you will need to get the install script and reinstall. yt is a Free and Open Source project, and we invite you to get involved. For more information, join the yt-dev mailing list, or see the hacking guidelines on the Wiki: http://yt.enzotools.org/wiki/HackingGuidelines . We anticipate several more releases in the 2.0 series as documentation and docstring coverage progress. Future developments will include an overhaul of the plotting system for intuitive generation of plots, a web-based notebook for remote analysis, better time series support, and inline analysis of running simulations. Please forward this announcement to any individuals or mailing lists you think may be interested. Sincerely, The yt development team: Matthew Turk Britton Smith Jeff Oishi Sam Skillman Stephen Skory John Wise Chris Malone John ZuHone Christopher Moody [View Less]

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yt-2.0 documentation uploaded
by Matthew Turk Jan. 14, 2011

Jan. 14, 2011

Hi everyone, I've uploaded a preliminary build of the new documentation for yt-2.0 here: http://yt.enzotools.org/doc/ (downloadable: http://yt.enzotools.org/doc/download.zip ) yt 2.0 will be released Monday. Please let me know any comments or suggestions you might have about the documentation -- if you see any problems, or any areas you think could use more information, or more emphasis, you'd like to help, etc etc, please feel encouraged to drop me a line. In particular, the orientation … [View More]

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periodic fixed res buffer
by John Wise Jan. 13, 2011

Jan. 13, 2011

Hi all, Is it possible to have a fixed resolution buffer with periodic boundary conditions, just like how the projections and slices are handled? I've tried to feed the argument periodic=True to the projection creation routine prj = pf.h.proj(dim, "Metallicity", weight_field="Density", periodic=True) frb = FixedResolutionBuffer(prj, region, (image_size, image_size)) where region is something like (-0.1,0.1,0.5,0.7) I've also tried setting the projection region to have boundaries within the … [View More]

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Re: [yt-users] yt-users Digest, Vol 35, Issue 17
by Liliana Altamirano Jan. 12, 2011

Jan. 12, 2011

hi! when I try to install yt and active cloning Enzo, i get this error: Installing yt Cloning a copy of Enzo. abort: No module named _ssl! yt installation it's ok, but enzo why not? liliana On Sun, 09 Jan 2011 10:35:21 -0800, yt-users-request wrote > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email,… [View More] send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > Today's Topics: > > 1. Re: The future of yt (Brian O'Shea) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 Jan 2011 08:31:30 -0500 > From: "Brian O'Shea" <bwoshea(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] The future of yt > Message-ID: > <AANLkTi=-35MyuuNY+KBy0MRK1G11wukNhMKoOoGOo_cM(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Matt, > > I know this is a couple days late, but I just wanted to respond to > say that it all sounds very sensible, and I am very excited to see > what the future of yt brings! > > --Brian > > On Fri, Jan 7, 2011 at 2:08 PM, Matthew Turk <matthewturk(a)gmail.com> > wrote: > > > Hi all, > > > > I'm writing today about a change in the way yt is being developed, > > which may have some visible changes. I want to start out by > > emphasizing that yt is, and will increasingly *be*, a *community* > > project driven by pragmatic needs for scientific analysis. Below I've > > outlined a couple of my future projects as well as a brief discussion > > of how to ensure that yt retains the community-developed approach that > > has served it very well over the last few years. > > > > As of January 1st, I've begun an NSF postdoctoral fellowship (the > > Office of CyberInfrastructure's "Transformative Computational Science" > > fellowship) designed to develop yt to the point that it can be used as > > a full integrated science environment, starting with the generation of > > initial conditions, moving through the conducting of a simulation, > > continuing with analysis (both post-processing and during the course > > of the calculation) and finishing with both scientific and outreach > > quality visualization. This will be driven forward most directly by > > my own studies of the formation of the first stars and galaxies, but > > it will also be conducted completely in the open and will be designed > > to provide a new mechanism for conducting simulations for the > > computational astrophysics community as a whole. These changes will > > be developed to be applicable to many different astrophysics codes, > > not just Enzo. My absence the last few weeks has been a result of > > this; I packed up and moved from San Diego to New York City and > > Columbia University. > > > > However, I need to emphasize that this won't just be me working in > > isolation for a few months and tossing things back at the source > > control repository: this project will live or die based on how well it > > is integrated into the workflows of others, and based on how engaged > > the other users and developers of yt are in the process of making > > these changes. If conducted in isolation, this project surely would > > fail; if conducted without the feedback from other working scientists, > > this project won't ever gain traction. This means that through the > > process of making decisions about the design and implementation of > > components up to and including initial deployment, I will be > > soliciting feedback, encouraging interaction and testing changes. As > > users and developers, you are free to be as involved with or as > > removed from this process as you desire. > > > > This new fellowship will result in several nearly immediate changes: > > > > 1) The oft-delayed 2.0 release: I will be putting out a 2.0 release, > > with the attendant documentation, by the 14th of January. This will > > mean the re-organized codebase will be the "stable" branch, and the > > cookbook and documentation will be updated to reflect this. > > > > 2) Documentation will be prioritized from here on out; I am dedicated > > to 100% coverage of yt.mods with docstrings, as well as newly written > > narrative documentation for yt. > > > > 3) A new system we're tentatively calling "the Forge" will be deployed > > to replace the ailing Barn, and I will focus on developing mechanisms > > for sharing of scripts and analysis tools. > > > > 4) Regression and answer testing will be run on a daily or weekly > > basis, to prevent errors and bitrot from creeping in. This will be > > initiated sometime in the couple weeks, hardware permitting. > > > > There will also be several more medium-term changes. > > > > 1) Outreach: yt and the yt community will aim to provide a bridge > > between scientists and outreach, by striving to enable both > > connections between outreach facilitators and by providing intuitive, > > narrative methods for visualization of astrophysical data. I am going > > to try to "bake in" narrative techniques into the visualization tools > > provided by yt. > > > > 2) The de-enzo-fication of yt will continue. Assumptions about the > > nomenclature, the data types and the content of data will be > > eliminated, and yt will continue to provide physically-motivated > > astrophysical analysis that abstracts the underlying data objects. > > > > 3) Blogging: I will strive to blog once a week on my progress toward > > these goals, on the Enzotools blog at blog.enzotools.org. > > > > As work progresses on the formal goals of the fellowship, I will > > update the mailing list, although I will attempt to keep the number of > > updates to a minimum on yt-users and keep both yt-dev and the > > Enzotools Blog as the main grounds for discussion. > > > > Thanks to all the other developers -- even though I wrote yt > > initially, it's a *community* project, and I do not see a future for > > it except as a community project. > > > > Best wishes, > > > > Matt > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > [View Less]

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The future of yt
by Matthew Turk Jan. 9, 2011

Jan. 9, 2011

Hi all, I'm writing today about a change in the way yt is being developed, which may have some visible changes. I want to start out by emphasizing that yt is, and will increasingly *be*, a *community* project driven by pragmatic needs for scientific analysis. Below I've outlined a couple of my future projects as well as a brief discussion of how to ensure that yt retains the community-developed approach that has served it very well over the last few years. As of January 1st, I've begun an … [View More]NSF postdoctoral fellowship (the Office of CyberInfrastructure's "Transformative Computational Science" fellowship) designed to develop yt to the point that it can be used as a full integrated science environment, starting with the generation of initial conditions, moving through the conducting of a simulation, continuing with analysis (both post-processing and during the course of the calculation) and finishing with both scientific and outreach quality visualization. This will be driven forward most directly by my own studies of the formation of the first stars and galaxies, but it will also be conducted completely in the open and will be designed to provide a new mechanism for conducting simulations for the computational astrophysics community as a whole. These changes will be developed to be applicable to many different astrophysics codes, not just Enzo. My absence the last few weeks has been a result of this; I packed up and moved from San Diego to New York City and Columbia University. However, I need to emphasize that this won't just be me working in isolation for a few months and tossing things back at the source control repository: this project will live or die based on how well it is integrated into the workflows of others, and based on how engaged the other users and developers of yt are in the process of making these changes. If conducted in isolation, this project surely would fail; if conducted without the feedback from other working scientists, this project won't ever gain traction. This means that through the process of making decisions about the design and implementation of components up to and including initial deployment, I will be soliciting feedback, encouraging interaction and testing changes. As users and developers, you are free to be as involved with or as removed from this process as you desire. This new fellowship will result in several nearly immediate changes: 1) The oft-delayed 2.0 release: I will be putting out a 2.0 release, with the attendant documentation, by the 14th of January. This will mean the re-organized codebase will be the "stable" branch, and the cookbook and documentation will be updated to reflect this. 2) Documentation will be prioritized from here on out; I am dedicated to 100% coverage of yt.mods with docstrings, as well as newly written narrative documentation for yt. 3) A new system we're tentatively calling "the Forge" will be deployed to replace the ailing Barn, and I will focus on developing mechanisms for sharing of scripts and analysis tools. 4) Regression and answer testing will be run on a daily or weekly basis, to prevent errors and bitrot from creeping in. This will be initiated sometime in the couple weeks, hardware permitting. There will also be several more medium-term changes. 1) Outreach: yt and the yt community will aim to provide a bridge between scientists and outreach, by striving to enable both connections between outreach facilitators and by providing intuitive, narrative methods for visualization of astrophysical data. I am going to try to "bake in" narrative techniques into the visualization tools provided by yt. 2) The de-enzo-fication of yt will continue. Assumptions about the nomenclature, the data types and the content of data will be eliminated, and yt will continue to provide physically-motivated astrophysical analysis that abstracts the underlying data objects. 3) Blogging: I will strive to blog once a week on my progress toward these goals, on the Enzotools blog at blog.enzotools.org. As work progresses on the formal goals of the fellowship, I will update the mailing list, although I will attempt to keep the number of updates to a minimum on yt-users and keep both yt-dev and the Enzotools Blog as the main grounds for discussion. Thanks to all the other developers -- even though I wrote yt initially, it's a *community* project, and I do not see a future for it except as a community project. Best wishes, Matt [View Less]

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izip not defined
by gso＠physics.ucsd.edu Jan. 7, 2011

Jan. 7, 2011

My script that called on extract_connected_set is running into a problem in the 2.0dev version of yt which was fine on my laptop running the old svn trunk. It said that izip is not defined. I looked around the source code and found some instances of izip, and they all called import before using it, so I tried to add from itertools import izip but that didn't work either. Am I just doing something wrong transitioning to 2.0? In the script, when calling pf.h.all_data(), it gives me the … [View More]

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