Mailman 3 January 2010 - yt-users

update that broke YT?
by gso＠physics.ucsd.edu 26 Jan '10

26 Jan '10

I was trying to run the halo finder in parallel this morning after updating YT and the particle IO stopped working. It was working last friday with YT version 1578. I have since reverted back to 1578 and made sure that it works. So the update made sometime in between caused this error. Can someone else please confirm the error? From G.S.

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yt Version 1.6 Release Announcement
by Matthew Turk 22 Jan '10

22 Jan '10

We're proud to announce the release of yt version 1.6, a point release of the analysis and visualization toolkit for Adaptive Mesh Refinement data. This release contains many small improvements to the codebase, as well as several large improvements. Most prominently, it features a completely redesigned, massively parallel implementation of the halo finding algorithm HOP, as well as attendant improvements to particle data IO and parallel communication. Additionally, the underlying data structures for hierarchical datasets have been rewritten for speed and clarity, enabling the future addition of new multi-resolution data formats to be easily added. yt features native support for Enzo (http://lca.ucsd.edu/projects/enzo) data, providing a natural and intuitive way to address physical regions in space as well as processed data. Some of the changes since yt-1.5 (released on November 3, 2009) include: * (New) Parallel HOP ( http://arxiv.org/abs/1001.3411 ) * (Beta!) Software ray casting and volume rendering (Sam Skillman has a gallery here: http://casa.colorado.edu/~skillman/simulation_gallery/simulation_gallery.ht… ) * Rewritten, faster and better contouring engine for clump identification * Spectral Energy Distribution calculation for stellar populations * Optimized data structures such as the hierarchy * Star particle analysis routines * Halo mass function routines * Completely rewritten, massively faster and more memory efficient Particle IO * Fixes for plots, including normalized phase plots * Better collective communication in parallel routines * Consolidation of optimized C routines into amr_utils * Many bug fixes and minor optimizations * Installation instructions, documentation, recipes, mailing list info and assorted other items can be found at the website, http://yt.enzotools.org/ along with an annotated changelog at http://yt.enzotools.org/doc/changelog.html . 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 . Sincerely, The yt development team: Matthew Turk Stephen Skory Britton Smith Jeff Oishi Sam Skillman Devin Silvia John Wise David Collins

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Re: [yt-users] Turbulent cascade
by Stephen Skory 15 Jan '10

15 Jan '10

Hi Libby, I've attached a quick shot at what you wanted. Please read through it and let me know if it does what you want and if I did something wrong (likely!), or if you don't understand why I did something. There is one subtlety that I should point out. It is statistically improper to consider a pair of points farther apart that 1/2 the shortest dimension of the box. Consider your starting point at the center of the box. If you look epsilon less than 1/2 of the shorted dimension of the box away towards the closest face, you're looking at a point near the periodic edge of the box. If you then look epsilon more than 1/2 the box edge past that previous point, you've reflected around the periodic boundary, and your *actual* distance is epsilon less than 1/2 because of the period. So, any distances greater than 1/2 the minimum box edge are statistically improper. I've also attached a plot which looks encouraging, I think! It would look smoother with more random points (bigger 'loopsize') I hope this helps! If it does, please let me know and I'll make it prettier and such and stick it into the yt codebase with documentation. _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Turbulent cascade
by Elizabeth Harper-Clark 15 Jan '10

15 Jan '10

Dear fellow YT-users, I would like to analyse turbulence in ENZO by comparing velocity difference at different scales. To do this I would like to calculate the velocity difference between each cell and cells a set distance bracket away, square, sum over all cells, and square root to get a turbulent velocity at that length scale. I would the like to do that for many different length scales to form a graph of turbulent velocity against length scale. Has anyone ever done anything like this with YT or have a suggestion for the easiest way to go about doing this? (with either SH = 1 or 0) Many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Astrophysics, UofT www.astro.utoronto.ca/~h-clark h-clark(a)cita.utoronto.ca AIM: edphc1 MSN: edphc1(a)hotmail.com Skype: eharperclark Office phone: 416-978-5759

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Callback: nparticles
by Elizabeth Harper-Clark 04 Jan '10

04 Jan '10

Hi guys, I want to use the nparticles rather than the particles callback so that I only plot PARTICLE_TYPE_MUST_REFINE (4). I am trying (full script at end of email): p.modify["nparticles"](1.0,p_ size=4.0, col='g', ptype='4') I tried with and without ' around the 4 but both times I get: Traceback (most recent call last): File "Density_movie.py", line 29, in <module> p.modify["nparticles"](1.0,p_size=4.0, col='g', ptype='4') File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-1.6dev-py2.5-linux-x86_64.egg/yt/raven/PlotTypes.py", line 52, in __getitem__ raise KeyError(item) KeyError: 'nparticles' Any idea what I am doing wrong? Many thanks, Libby Density_movie.py: from yt.mods import * import pylab import sys import cmath import matplotlib.ticker # # Code to make the frames for a movie showing density projection # rho_min = 1.e-22 rho_max = 1.e-32 frame_template = "aaWoC/%s/densityframe_%01i_%04i" for n in range(12,200): # make density projection with particles on #pf = lagos.EnzoStaticOutput("WOCbin/%s/DD%04i/data%04i" % (sys.argv[-1],n, n)) pf = lagos.EnzoStaticOutput("WOCbin2/%s/DD%04i/data%04i" % (sys.argv[-1],n, n)) #print pf.h.field_list pc = raven.PlotCollection(pf, center=(0.5,0.5,0.5)) time = pf["InitialTime"]*pf["years"] for ax in range(1): p = pc.add_projection("Density", ax, weight_field="Density") #pc.set_zlim(rho_min, rho_max) p.set_cmap('hot') sp = pf.h.all_data() colours = sp["ParticleMassMsun"] if sp["ParticleMassMsun"].size > 0: p.modify["nparticles"](1.0,p_size=4.0, col='g', ptype='4') p.modify["text"]((0.1,0.9),"time = %i years" % (pf["InitialTime"]*pf["years"]), text_args = {'color':'w'}) #p.set_width(0.1, 'pc') pc.save(frame_template % (sys.argv[-1],ax,n), override=True) -- Elizabeth Harper-Clark MA MSci PhD Candidate, Astrophysics, UofT www.astro.utoronto.ca/~h-clark h-clark(a)cita.utoronto.ca AIM: edphc1 MSN: edphc1(a)hotmail.com Skype: eharperclark Office phone: 416-978-5759

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yt-users January 2010