Mailman 3 February 2014 - yt-users

rainbow+white?
by Stephanie Tonnesen 18 Feb '14

18 Feb '14

Hi yt-users, I am imagining that this is something silly, but I tried to use rainbow + white, and it seems to me that it is actually rainbow + black? Certainly on the colormaps page those two maps look identical: http://yt-project.org/docs/dev/visualizing/colormaps/index.html?highlight=c… Is this actually the case? is there just some simple pointer that is messed up somewhere? Or can someone point me to the white in rainbow+white? Thanks! Stephanie

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yt for PLUTO
by Varadarajan Parthasarathy 17 Feb '14

17 Feb '14

Salutations, I am Varadarajan Parthasarathy, PhD student at CAMK, Warsaw. I am currently using PLUTO for simulating accretion discs. I have output in data.nnnn.dbl.h5 (essentially HDF5 files) format. Can I get the guidance for loading this data and doing data analysis or producing some videos and plots in yt. I came across the PLUTO-specified field list, but it was difficult to get all the information from it. It would be helpful if I get some ideas on this. Regards, Varadarajan

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Pickling YT objects
by Sam Geen 14 Feb '14

14 Feb '14

Hi, I'm making plots of my data and I want to save them as pickle files so I can load them later and perhaps mess with the colour map limits, say, without reprocessing all the data (I have about 9TB to go through). When I tried this I got the error: "TypeError: can't pickle instancemethod objects" Do you know if this is possible, or some variant of it? I'm running: pf = yt.mods.load(file_location) prj = yt.mods.ProjectionPlot(pf, 2, var, center=[0.5, 0.5, 0.5], width=(rlim, 'pc'), weight_field=None) and trying to pickle prj, when I get the error. prj appears to be a yt.visualization.plot_window.ProjectionPlot object and not an instance method, but I could be wrong. At least it could be good to save the 2D image array and link it back later to a YT plot object, but I don't know much about the internal workings of the plot objects as to whether this is possible or not. Thanks, Sam

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animations in IPython notebooks?
by Brian O'Shea 14 Feb '14

14 Feb '14

Hi yt-users, I've been playing around with Jake VanderPlas's JSAnimation package for making animations in IPython notebooks [1], and have been pretty impressed with it. I'd like to use this in a class I'm teaching - in particular, with yt and (preferably) astrophysical data. Does anybody have a good example of using yt + JSAnimation to make animations? And, if so, would you be willing to share? Thanks! --Brian [1] http://jakevdp.github.io/blog/2013/05/19/a-javascript-viewer-for-matplotlib…

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Lightray object creation problem
by Pengfei Chen 13 Feb '14

13 Feb '14

Hi all, I've got enough history dumps and some redshift dumps from Enzo but when I tried to use them to create a lightray object, I got a problem: The code I use is: lr = LightRay("/scratch/01041/tg802953/BKGRD800B/HD4760/HD4760", 'Enzo', 3.0, 5.0, use_minimum_datasets=True) And I have enough HDXXXX datasets. But I still get the following error: P000 yt : [ERROR ] 2014-02-06 20:32:53,057 Cosmology splice incomplete due to insufficient data outputs. I've done this with another simulation which has enough RDXXXX outputs before and it worked well. So I wonder how could the LightRay recognize HDXXXX datasets. Thanks, Pengfei

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RAMSES MHD visualisation weirdness
by Sam Geen 12 Feb '14

12 Feb '14

Hi, I tried visualising a RAMSES MHD output in YT and got this weird effect: http://i.imgur.com/abjRorm.png (this happens for slices and projections) Any idea what could be causing this? Nearly-identical non-MHD simulations seem to visualise fine, and it happened for every MHD output I've looked at. I can give more info if you like, although I'm not sure what diagnostics to check for, so pointers on how to hunt this down would be appreciated as well! It's entirely possible it's a bug/side-effect of the MHD solver, although I'm not sure what, and other visualisation routines (in IDL/Fortran) seem to work fine with some of the outputs I've tried on it. Thanks, Sam

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combining read in files in yt
by Desika Narayanan 11 Feb '14

11 Feb '14

Hi All, (a second question, though in a different thread for cleanliness): Is it possible to combine multiple files that I load into yt? i.e. if I have particle lists that are written into multiple files and do: >pf1 = load("snap1a.hdf5") >pf2 = load("snap1b.hdf5") Is it possible to combine the two into a single pf that contains the information for all of the particles? thanks, desika

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halo finding on non DM particles
by Desika Narayanan 11 Feb '14

11 Feb '14

Hi All, I have a quick question on halo finding - is it possible with the HOP halo finder in yt to link gas particles instead of DM particles? (even if they have different masses)? If so, is there a specific keyword to include? (i.e.: http://paste.yt-project.org/show/4304/ ) Thanks -desika

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Announcement: 2014 UC-HIPACC yt workshop, March 23-25
by Matthew Turk 10 Feb '14

10 Feb '14

Dear Colleagues, We are proud to officially announce the upcoming 2014 yt developer workshop. This three day event, to be held on the campus of the University of California, Santa Cruz on Sunday March 23rd through Tuesday March 25th, will bring together a diverse group of students, researchers, and developers. While past workshops have been broad in scope, this workshop will be focused on advancing the goals of yt 3.0 in tandem with the goals of the AGORA project. The four primary goals of this workshop will be to advance the state of the code for: * GPU-based rendering, integrating the PyRGBA toolkit developed at UCSC * Improve scalability of particle and octree datasets in yt * Streamline and optimize SPH smoothing kernel implementations * Integrate more tightly with halo finders and develop an API for SAM interop Through UC-HIPACC we are able to offer attendance funding for participants, including travel and lodging. Funds will be preferentially distributed to students and the level of individual support will depend on demand. If you are interested in attending, please fill out this very short form, and we will be in touch shortly with more details: http://goo.gl/ZDfFvI If you have questions or concerns about the workshop, please feel free to contact the organizers at workshop2014(a)yt-project.org. On behalf of the organizing committee, Matthew Turk Miguel Rocha Alex Bogert

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AMR iscontour flux units
by Nathan Goldbaum 07 Feb '14

07 Feb '14

Hi all, I have a question about the calculate_flux function defined for AMRSurface objects. The docstrings for calculate_flux note that the returned fluxes are the code unit area multiplied by the local flux density. I'm curious what this means for AMR simulations, where the 'area' will depend on the local resolution. Does the fluxing calculation account for that? What about isocontours that cross level boundaries? Thanks for your advice, Nathan

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