Mailman 3 - yt-users

Changes to the trunk
by Matthew Turk 20 Nov '09

20 Nov '09

Hi there, Tonight I'm merging a bunch of changes from me, Britton Smith, John Wise and Stephen Skory back into the trunk from the mercurial repository. If you're running on the yt-1.5 source tree, this won't affect you -- but if you're running on trunk, the next time you update you will have to rerun "python2.6 setup.py develop" or "python2.6 setup.py install" depending on how you installed. If you used the install script, you should also be able to re-run it at any time to get an updated source tree and installation. There are no pressing fixes in this, only speed and memory improvements, so don't feel it's necessary to make the jump just now if you're happy with where you are. If you do update, here's a minor changelog: * Hierarchy is much faster, and the .yt file now only stores data products, all hierarchy info goes into a .harrays file (for forward compatibility with Enzo) * The attributes off the hierarchy for grids: gridLeftEdge and gridRightEdge are now grid_left_edge and grid_right_edge, in keeping with our coding standards * Hierarchy has been rewritten for *clarity* * The bug with DM-only sims has been fixed * IO routines have been refactored and very cleaned up * Preliminary particle IO readers have been added -- much, much faster, but not yet production-ready * New cloud-in-cell deposit function without needing fortran * Some other minor things to support coming features All the public and primary functions, classes etc should be the same. Thanks, and let us know if there are ANY problems! -Matt

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Find clumps - callback
by Elizabeth Harper-Clark 19 Nov '09

19 Nov '09

Hi Guys, I am (trying) to use the find_clumps routine to identify clumps in my data and I would then like to visualize it. How do I get the data from the find_clumps routine into the callback: p.modify["clumps"]() so I can put it on projections/slices? What should it then look like? 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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corrupt enzo restart file?
by Stephen Skory 16 Nov '09

16 Nov '09

Hi all, I am getting this error <http://paste.enzotools.org/show/257/> when I attempt to instantiate the grid hierarchy. Here is my restart file <http://paste.enzotools.org/show/258/> and the corresponding hierarchy file <http://paste.enzotools.org/show/259/>. Does anyone see anything obviously wrong? I'm attempting to analyze a DM-only run with 2x grid to particle resolution, so I might have fudged something up. Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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yt Version 1.5 Release Announcement
by Matthew Turk 03 Nov '09

03 Nov '09

We're proud to announce the release of yt version 1.5, an analysis and visualization toolkit for Adaptive Mesh Refinement data. 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. Version 1.5 features many new improvements, most prominently that of the addition of parallel computing abilities and generalization for multiple AMR data formats. Additional improvements include: * Fully rewritten documentation, featuring a new cookbook with downloadable recipes and commenting facilities * Extensive methods section of documentation * Fully parallel slices, projections, cutting planes, profiles, quantities * Parallel HOP halo finder * Friends-of-friends halo finder * Object storage and serialization * Major performance improvements to the clump finder (factor of five) * Generalized domain sizes * Generalized field info containers * Dark Matter-only simulation support * 1D and 2D simulation support * Better IO for HDF5 sets * Support for the Orion AMR code * Spherical re-gridding of data * Automated halo profiler and imager * Limited non-axially aligned projection support ("disk stacking") * Light cone generator * Callback interface improved * Several new plot overlay callbacks * New data objects -- ortho and non-ortho rays, limited ray-tracing * Fixed resolution buffers * Spectral integrator for CLOUDY data * Substantially better interactive interface * Performance improvements *everywhere* * Command-line interface to *many* common tasks * Isolated plot handling, independent of PlotCollections Installation instructions, documentation, recipes, mailing list info and assorted other items can be found at the website, http://yt.enzotools.org/ . This release is the product of a year of work by the development team, and we are very proud of the results and happy with what we have to offer. Thanks very much! Sincerely, The yt development team: Matthew Turk Britton Smith Jeff Oishi Stephen Skory Sam Skillman Devin Silvia John Wise David Collins

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Ignore last post
by Nicholas Earl 20 Oct '09

20 Oct '09

Sorry everyone! That last post was a failed email in my outbox that somehow got sent; please ignore! Thanks for all your help! Nicholas Earl

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Ignore last post
by Nicholas Earl 20 Oct '09

20 Oct '09

Sorry everyone! That last post was a failed email in my outbox that somehow got sent; please ignore! Thanks for all your help! Nicholas Earl

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Simple radial profile
by Nicholas M. Earl 19 Oct '09

19 Oct '09

Hey all, I was hoping that someone might have a suggestion or answer for an issue I'm having with generating simple radial profiles from simulation data. The profiles automatically generate axis bounds and while I can set the bounds on the x axis using the x_bounds parameter, I don't know how, or if it's even possible, to set a similar restriction for the y axis. (I have tried simply setting a y_bounds parameter, but the script breaks stating that y_bounds is unrecognized). Here is an example of the code: from yt.mods import * # set up our namespace for n in range(1,242): pf = load("/work/01198/earln/RSW_nC_1-0/DD%04i/DD%04i" % (n,n)) pc = PlotCollection(pf, center=[0.5, 0.5, 0.5]) pc.add_profile_sphere(10.0, "mpc", ["Radius", "RadialVelocity"], weight="CellMassMsun", x_bounds=(1.0e+18,1.0e+20), y_bounds=(1e-3, 1.e+8)) pc.save("/work/01198/earln/RSW_nC_1-0/graph-data_radvel/ profiles/%s" % pf) Any suggestions or help would be greatly appreciated, Nicholas Earl

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Simple radial profile
by Nicholas M. Earl 14 Oct '09

14 Oct '09

Hey all, I was hoping that someone might have a suggestion or answer for an issue I'm having with generating simple radial profiles from simulation data. The profiles automatically generate axis bounds and while I can set the bounds on the x axis using the x_bounds parameter, I don't know how--or if it's even possible--to set a similar restriction for the y axis. (I have tried simply setting a y_bounds parameter, but the script breaks stating that y_bounds is unrecognized). Any suggestions or help would be greatly appreciated, Nicholas Earl

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Building latex documentation with sphinx
by LUK ShunTim 06 Oct '09

06 Oct '09

Hi, Sorry if this is the not appropriate list for yt-docs. I can't find one. While trying to build the latex documentation with sphinx (using a hg check out), I got a lot of warnings like "/home/0/00work/amr/yt/yt-doc-hg/yt-doc/source/cookbook/aligned_cutting_plane.rst:: WARNING: image file not readable: cookbook/_aligned_cutting_plane/aligned_cutting_plane_RedshiftOutput0005_CuttingPlane__Density.png" and make all-pdf in the _build/ directory failed with messages like "!pdfTeX error: pdflatex (file cookbook/_simple_slice/simple_slice_RedshiftOutput0005_Slice_x_Density.png): cannot find image file" How can it be fixed? Regards, ST --

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Problem with zlim setting in yt slices
by Fen Zhao 15 Sep '09

15 Sep '09

Hi all, I've recently been having problems setting the colorbar max and min in yt, and would appreciate some help figuring out what the problem might be. Full python code attached at the end, but the important parts are: pf=lagos.EnzoStaticOutput(thefile) pc = PlotCollection(pf, center=[c1, c2, c3]) plot1=pc.add_slice("B", 0) plot2=pc.add_slice("Density", 0) plot3=pc.add_slice("Velocity_Vorticity1", 0) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) +"large" pc.save(thefile2) plot1.set_width(haloradius*2,1) plot2.set_width(haloradius*2,1) plot3.set_width(haloradius*2,1) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) + "halo" pc.save(thefile2) Neither the "large" or "halo" have the colorbar set correctly. Cheers, Fen Context of code: import sys sys.path = ["/usr/work/mturk/local-testing/lib/python2.5/site-packages/"] + \ sys.path from yt.config import ytcfg; ytcfg["lagos","serialize"] = "False" from yt.mods import * #import yt.lagos as lagos #import yt.raven as raven #import os.path def write_out_binned_vals(plot, fn): vals = plot.vals x = plot.x_bins y = plot.y_bins print "Opening",fn, vals.shape, x.shape, y.shape f=open(fn,"w") for i in range(x.shape[0]): for j in range(y.shape[0]): print i,j f.write("%0.5e\t%0.5e\t%0.5e\n" % (x[i],y[j],vals[i,j])) f.close() #ind=71 #inputDir="/a/wain027/g.ki.ki01/fenzhao/data/nobackup/vorticity/correct" inputDir="/lustre/ki/orange/fenzhao/vorticity/try2" outputDir="/a/wain027/g.ki.ki01/fenzhao/data/nobackup/vorticity/analysis/slices/data/images/other" outputName="lustreversion" start=40 end=40 ind=start while ind<=end: thefile= inputDir + "/star_%04i.dir/star_%04i" % (ind,ind) output= outputDir + "/" + outputName+ "%04i" pf=lagos.EnzoStaticOutput(thefile) timeUnits=pf["years"] DensityUnits=pf["Density"] LengthUnits=pf["cm"] VelocityUnits=pf["x-velocity"] newred=pf["CosmologyCurrentRedshift"] a=1/(1+newred) k=1.3806503e-16 c=2.99792e10 e=4.8032068e-10 me=9.1093897e-28 mh=1.66053886e-24 pressure=k*(DensityUnits/mh) density=DensityUnits/mh graddensity=density/LengthUnits gradpressure=pressure/LengthUnits bbunits=(c/e)*graddensity*gradpressure/(density**2) vorticityUnits=VelocityUnits/LengthUnits alpha=mh*c/e/(1+1e-4) def Vorticity(field,data): return (((data["Velocity_Vorticity1"]**2)+(data["Velocity_Vorticity2"]**2)+(data[" Velocity_Vorticity3"]**2))**0.5)*vorticityUnits lagos.add_field("Vorticity", units=r"\rm{s}^{-1}",function=Vorticity) import numpy as na def B(field, data): return na.clip(alpha*(data["Vorticity"]),1e-30,1e30) lagos.add_field("B", units=r"\rm{Gauss}", function=B) haloradius=0.013 halo = pf.h.sphere([0.5, 0.5, 0.5], haloradius*2.0) v, i, c1, c2, c3, gi = halo.quantities["MaxLocation"]("Density", lazy_reader=True) pc = PlotCollection(pf, center=[c1, c2, c3]) plot1=pc.add_slice("B", 0) plot2=pc.add_slice("Density", 0) plot3=pc.add_slice("Velocity_Vorticity1", 0) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) +"large" pc.save(thefile2) plot1.set_width(haloradius*2,1) plot2.set_width(haloradius*2,1) plot3.set_width(haloradius*2,1) plot3.set_log_field(False) plot3.set_zlim(-200, 500) thefile2=(output % ind) + "halo" pc.save(thefile2) ind=ind+1 #plot=pc.add_slice("B", 0)

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