Mailman 3 October 2014 - yt-users

accessing the row simulation data using yt
by Junhwan Choi (최준환) 03 Oct '14

03 Oct '14

Hi yt user, I have one basic question how I can access row data using yt. For example, I would like to access finset cell information and manipulate form it. Does following script print the x, y, z, vx, vy, vz, and mass for all finest cells in the spherical region? ================= from yt.mods import * pf = load("../DD%04d/DD%04d" % (snapshot,snapshot)) center = pf.h.find_max("Density")[1] sp = pf.h.sphere(center, (rmax,'pc')) for icell in range(0,sp["CellMassMsun"].size): print sp["x"][icell], sp["y"][icell], sp["z"][icell] print sp["x-velocity"][icell], sp["y-velocity"][icell], sp["z-velocity"][icell] print sp["CellMassMsun"][icell] ================ I know that this kind of the procedure violate the bases of yt philosophy. However, it is sometimes useful, particularly when I want to compute very specific quantities. If you have other suggestion regarding to access simulation raw data in yt way, please let me know. Thank you, Junhwan

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ANN: Grackle 2.0 release
by Britton Smith 01 Oct '14

01 Oct '14

Greetings, I am very happy to announce the release of the Grackle chemistry and cooling library version 2.0! The Grackle is a library for chemistry and radiative cooling in astrophysical simulations. This release has the same functionality as version 1.0, but features a new, easier to implement interface with a variety of working examples for C, C++, and Fortran codes. The user is no longer required to carry around the internal data structures, making integration with simulation codes even simpler. The internal machinery has been made more robust and can now be run reliably in both 32 and 64-bit modes. The documentation has also been significantly expanded and improved. For more information, see here: http://grackle.readthedocs.org/en/grackle-2.0/ In addition to the 2.0 release, we are simultaneously releasing version 1.1, which contains a few bug fixes and enhancements to the original 1.0 interface. If your code uses version 1.0, it is recommended that you update to version 1.1, which can be done by cloning a copy of the Grackle repo and updating to the 1.1 version with: https://bitbucket.org/grackle/grackle cd grackle hg up grackle-1.1 The documentation for Grackle 1.1 can be viewed at: http://grackle.readthedocs.org/en/grackle-1.1/ Both Grackle 1.1 and 2.0 also feature the following enhancements: - updated H-, H2, and HD chemistry and cooling rates from Simon Glover - an option to build either static or dynamic libraries - the sign of the cooling time is now preserved allowing the user to discern between heating and cooling - pre-made make files for NASA Pleiades, TACC Stampede, and NCSA Blue Waters The Grackle can be obtained at: https://bitbucket.org/grackle/grackle The documentation can be seen here: http://grackle.readthedocs.org/en/latest/ Thanks to everyone who contributed to the release! Regards, Britton and the Grackle dev team

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Re: [yt-users] install failure
by Mordecai-Mark Mac Low 01 Oct '14

01 Oct '14

Hi Matt, good call! importing matplotlib.pyplot resulted in an abort out of python to the shell prompt: bash-3.2$ which python /Users/mordecai/bin/yt-x86_64/bin/python bash-3.2$ python Python 2.7.8 (default, Sep 28 2014, 20:55:56) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> import matplotlib.pyplot Abort trap: 6 bash-3.2$ python Python 2.7.8 (default, Sep 28 2014, 20:55:56) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import h5py >>> - Mordecai On Oct 1, 2014, at 9:20, <yt-users-request(a)lists.spacepope.org> <yt-users-request(a)lists.spacepope.org> wrote: > Date: Sun, 28 Sep 2014 21:43:38 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Fwd: install failure > Message-ID: > <CALO3=5Ew7ni1YAdn1V8zUPfOG0U8OA3+PR_Su97gbntA3A8nkw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Mordecai, > > On Sun, Sep 28, 2014 at 9:04 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: >> >> >> On Sun, Sep 28, 2014 at 6:57 PM, Mordecai-Mark Mac Low <mordecai(a)amnh.org> >> wrote: >>> >>> Here?s are examples of the problem. yt fails immediately with any usage. >>> As you can see, I don?t have a lot of information here! >>> >>> >>> [yt-x86_64] sagittariusb 1 % yt >>> Abort >>> [yt-x86_64] sagittariusb 2 % yt --help >>> Abort >>> [yt-x86_64] sagittariusb 3 % python >>> Python 2.7.8 (default, Sep 28 2014, 20:55:56) >>> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> import yt >>> Abort >>> [yt-x86_64] sagittariusb 4 % >> > > My guess, which could be far off, is that it's a module yt is > importing. I would try these things: > > import numpy > import matplotlib.pyplot > import h5py > > and see if any of those error out. If they don't, then I'll send over > a script importing each component of yt which you can run which will > identify which particular submodule. I suspect a symbol is unresolved > or causing some issue; we often see similar behavior on systems where > the linking is tricky. > > -Matt > > -- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA

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Python SSL failure, yt3, osx
by David Collins 01 Oct '14

01 Oct '14

Hi, Everybody-- I have a potentially dumb question. I'm installing yt3.0 (a fresh install) on osx 10.9, and I get the following error. It looks like the error is coming from the hg clone, for some reason the newly installed python can't find SSL. I can use another install of hg on this machine just fine. Has anyone else seen this, and do you know if there's an easy fix? Thanks! d. Using curl Using shasum -a 512 Cloning yt Setting YT_DIR=/Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ Installing distribute ******************************************** FAILURE REPORT: ******************************************** abort: repository /Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ not found! /Users/dcollins/local-2014-09-23-yt3/bin/python2.7: can't open file '/Users/dcollins/local-2014-09-23-yt3/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: Python SSL support not found using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: Python SSL support not found abort: repository /Users/dcollins/local-2014-09-23-yt3/src/yt-hg/ not found! /Users/dcollins/local-2014-09-23-yt3/bin/python2.7: can't open file '/Users/dcollins/local-2014-09-23-yt3/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory -- -- Sent from a computer.

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