Mailman 3 August 2014 - yt-users

yt-3.0 density gradient
by Lile Wang 09 Aug '14

09 Aug '14

Hi all, I am just worried about the problem associated to the density gradient field in yt-3.0. When I was trying to get the gradient of density field along z (actually any) direction, I got this error message (last few lines) when calling data[ 'density_gradient_z' ]: ~/lilew/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in selector(self) 529 if sclass is None: 530 raise YTDataSelectorNotImplemented(self._type_name) --> 531 self._selector = sclass(self) 532 return self._selector 533 ~/lilew/yt-x86_64/src/yt-hg/yt/geometry/selection_routines.so in yt.geometry.selection_routines.RegionSelector.__init__ (yt/geometry/selection_routines.c:20276)() RuntimeError: Error: bad Region in non-periodic domain along dimension 0. Region left edge = -0.01171875 code_length, Region right edge = 0.13671875 code_lengthDataset left edge = 0. 0 code_length, Dataset right edge = 1.0 code_length Similar things happen for the pressure gradient. The data input was generated by Enzo with AMR. In comparison, it works well with yt-2.6, where I refer to the gradient by data[ 'gradDensityZ' ]. Any ideas are appreciated. Thanks! Cheers, Lile ----------------------------------------------------------- Lile 'Patrick' Wang Dept. of Astroph. Sci., Princeton University, NJ 08544 USA Website : http://www.astro.princeton.edu/~lilew/ <http://www.astro.princeton.edu/%7Elilew/> Tel (Mobile): +1-(734)-834-3936 Tel (GVoice): +1-(510)-926-6831 -----------------------------------------------------------

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ANN: Enzo 2.4 Release
by Nathan Goldbaum 08 Aug '14

08 Aug '14

We are pleased to announce the release of version 2.4 of the Enzo code. This is a periodic release that includes all changes committed to the Enzo BitBucket repository since July 2013. This release contains some new features and a number of enhancements and bugfixes. Enzo now has bindings to version 1.0 of the grackle chemistry and cooling library. Grackle is based on Enzo's own cooling and chemistry code and includes updated rate and chemistry tables, as well a number of enhancements and new features that are not available in Enzo's native chemistry and cooling modules. Enzo's solvers and physics modules have also seen improvements, including updates for the GPU MHD solver, the FLD solver, and the MHD-CT solver, the Jeans pressure floor, the Cen & Ostriker star particle, tracer particles, and particle splitting. There have also been a number of infrastructure improvements, including a new progress meter script (which allows the user to monitor simulations during runtime), updates for geometric refinement regions and the shear refinement criterion, improved control over the frequency of hierarchy rebuilds, updates for test problem initialization (which is now more memory efficient), and improvements to the GalaxySimulation, KelvinHelmholtz, and CosmologySimulation problem types. There is also a new rotating turbulent sphere problem type. There have also been a number of significant bugfixes, including several that may increase the stability and efficiency of production multi-physics simulations. We urge all users to update to the latest version if they are using Enzo 2.3 or earlier. While one can obtain the release by downloading a tar file, we strong encourage all users to use enzo from a clone of the mercurial repository, which will facilitate reproducible work with the code. For more information about enzo, see http://enzo-project.org. For the release notes and changelog, see http://enzo-project.org/ReleaseNotes.html On behalf of the Enzo collaboration, Nathan Goldbuam

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Generation of smoothing lengths from coordinates of tracer particles
by Amos Manneschmidt 08 Aug '14

08 Aug '14

Hello, I am a student researcher working on the Chimera project. Part of my work involves creating density maps from tracer particles that accurately represent what we get directly interpolated to the grid from chimera code. If I can do this I know I can make accurate element abundance maps for up to 150 species. We are limited by computing resources to creating maps for only 14 species directly. Here is a video of the best conservative density plot I have been able to come up with thus far. The smoothing lengths for the tracers are found in a round-about way right now that is less than ideal. Is there a way in yt to create smoothing lengths using just particle coordinates like this? (IE the complex nearest neighbor math I would rather not code myself if I don’t have to) Thanks, Amos M

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doing SPH smoothing without smoothing lengths (or with them inputted manually)
by Brendan Griffen 08 Aug '14

08 Aug '14

Hi, As I understand yt is able to construct an array based on cloud-in-cell assignment but not using sph assignment. Each particle must have their own smoothing lengths. Could a rudimentary smoothing length be assigned within yt if particles don't already have a smoothing length? The volume rendering looks great for gas with a 'density' field but if I want to create a sph smoothed field also called 'density' for the dark matter particles, my only option for particle data at this point is cloud in cell assignment? This looks OK for large scale full homogeneous runs but for zoom-ins cloud in cell looks pretty terrible. Or could you even feed yt the smoothing lengths (say output from subfind) as a vector which yt then uses for the sph assignment? This might be a good first step as I already have the smoothing lengths pre-calculated in hsml files from subfind. Thanks. Brendan

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coLaboratory Chrome App
by Sam Skillman 08 Aug '14

08 Aug '14

Hi all, Some of you might be interested in a few news bits today: http://googleresearch.blogspot.com/2014/08/doing-data-science-with-colabora… and http://www.symmetrymagazine.org/article/august-2014/open-access-to-the-univ… What's even cooler than the fact that you can now load up an ipython notebook that runs sandboxed in your Chrome browser is that because Matt is the one compiling all these python tools into the Chrome app, we went ahead and included a very recent version of yt 3.0! Then we went a bit further, and baked in thingking ( https://bitbucket.org/zeropy/thingking) and some DarkSky tools, so when you put it all together now anyone and everyone can access data from the DarkSky simulations. If you install the chrome app ( https://chrome.google.com/webstore/detail/colaboratory-notebook/pianggobfjc…) then check out some examples: Dark Sky Examples <https://docs.google.com/folderview?id=0B7ET8zdoN208T1ZRNnk4cUJ0YnM&usp=driv…> We (Matt, Mike Warren, and I) would love to hear feedback if you try things out. I expect there will some growing pains with the interface, but we're all pretty excited about finally getting this out. Congrats to Matt and the Chrome/Jupyter teams! Cheers, Sam

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troubles with derived field: 1+1 is not equal to 2
by Antoine Strugarek 08 Aug '14

08 Aug '14

Hello, I’m new to yt so this maybe solved easily, though it puzzled me for quite some time and I still don’t understand what is going on. I try to create derived fields to analyze a simulation using AMR, from an output from CHOMBO. I define the following derived fields: def _VRA(field,data): return data['Cylsin']*data['Vx2'] def _VRB(field,data): return data['Cylcos']*data['Vx1'] def _VVR(field,data): return data['VRA']+data['VRB'] Then I add them to my yt object: ds=yt.load(file) ds.index ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=False) ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=False) ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=False) and everything goes on smoothly (they are the only variables named this way). Now, If I try to slice VRA and VRB I obtain the (correct) attached plots. Both VRA and VRB are strictly positive. If I try to slice VVR which is the sum VRA+VRB, I obtained the third attached plot which does not correspond to the expected sum (there are even negative values)! I suspect something went odd in the slice function, but I used the exact same lines of code to generate the three plots. I must be missing something here but I really don’t get it. Many thanks in advance for your help! Antoine Antoine STRUGAREK ------------------------------------------------------------------- Webpage Département de physique, Université de Montréal strugarek(a)astro.umontreal.ca (+1) 514 343 7077 -------------------------------------------------------------------- DSM/IRFU/SAp/LDEE CEA Saclay DSM/IRFM/SCCP CEA Cadarache antoine.strugarek(a)cea.fr --------------------------------------------------------------------

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yt python import error
by Romeel Davé 07 Aug '14

07 Aug '14

Has anyone seen an error like this? I go into python and say "import yt" and it gives http://paste.yt-project.org/show/4994/ The problem seems to be with PyUnicodeUCS2_DecodeUTF8, and it also appears when i try to pip install scipy using yt's python. I am using anaconda, and uname -a gives Linux ursa.uwc.ac.za 3.9.10-100.fc17.x86_64 #1 SMP Sun Jul 14 01:31:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux romeel

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Animation of annotated projection plot
by Hao Wang 05 Aug '14

05 Aug '14

Hi all, I have been trying to make a movie out of annotated projection plots but encountered the following problem: ------------error message----------------------------- File "...../yt/src/yt-hg/yt/visualization/plot_modifications.py", line 1157, in _get_region LE[zax] = data.center[zax] - self.width*0.5 TypeError: 'NoneType' object has no attribute '__getitem__' -------------------------------------------------------------- I pasted the script (copied from the yt Cookbook) I used below. It worked fine without the "prj.annotate_particles(1.0)" line. The annotation itself works too -- the figure looks good in the IPython notebook. ======Script (anim.py)================================== import matplotlib.animation as anim from matplotlib.backends.backend_agg import FigureCanvasAgg from yt.mods import * prj = ProjectionPlot(load('DD0000/DD0000.hierarchy'), "z", 'Density') prj.annotate_particles(1.0) # adding this line causes error fig = prj.plots['Density'].figure fig.canvas = FigureCanvasAgg(fig) def animate(i): filename = './DD%04i/' % i + 'DD%04i' % i + '.hierarchy' pf = load(filename) prj._switch_pf(pf) density_ani = anim.FuncAnimation(fig, animate, frames=100, interval=100, blit=False) density_ani.save('density_animation.mp4') ==================== Could anyone point out the problem? Thanks in advance, Hao

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Current branches post yt-3.0 and "yt update"
by Matthew Turk 05 Aug '14

05 Aug '14

Hi all, I wanted to write with a brief update on a few things. Now that yt-3.0 has been released, we have changed the way named branches work in the yt repository. * yt-2.x => This is what used to be the "yt" branch, and is legacy yt 2.x support. * yt-3.0 => This branch is deprecated, but not closed, and will not be undergoing regular updates * yt => This is the new development branch, which is now "yt 3.0" This will become yt 3.1. * stable => This is the stable branch (as before) which now corresponds to yt-3.0 stable releases. If you do not use the "yt update" functionality, you may disregard the remainder of this email. If you have been running yt 2.x, and want to stay on yt 2.x, you will need to make a one-time modification to your source directory. NOTE : ANY UNCOMMITTED CHANGES WILL BE WIPED OUT BY THIS COMMAND. 1) Activate your yt environment (typically via the activate script) 2) cd $YT_DEST/src/yt-hg 3) hg pull 4) hg up -C yt-2.x That will switch you to the yt-2.x branch. If you have been running yt 3.0, you will need to make a similar modification: 1) Activate your yt environment (typically via the activate script) 2) cd $YT_DEST/src/yt-hg 3) hg pull 4) hg up -C yt Hope that helps! -Matt

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Loading gadget snapshot
by Jared Coughlin 05 Aug '14

05 Aug '14

Hello! I'm a grad student working with gadget, and someone told me today about version 3, which supports gadget! I have never used yt before, as it has never supported sph before, so if this is a really stupid question, please forgive me. I followed the bootcamp examples just fine, and then tried to load in a gadget snapshot (obtained from the sample datasets portion of yt's website) by doing yt.load("snapshot_010"). I got the following error: yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('snapshot_010',) {}, but could not load! Then I tried yt.load("snapshot_010", "gadget_binary"), but got the same error. Clearly, I am misunderstanding something very important here. I looked at the source and saw the GadgetBinaryFile class, so I know it can be done, I just can't figure out how. Very sorry for the bother. Any help would be greatly appreciated! Thank you very much! -Jared

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yt-users August 2014