Mailman 3 September 2014 - yt-dev

yt workshop hotel share?
by Nathan Goldbaum 22 Sep '14

22 Sep '14

Hi all, Does anyone going to the yt workshop want to share hotel rooms? I'm planning on flying in on the 15th and checking out on the 18th. -Nathan

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Call for blog posts
by Matthew Turk 22 Sep '14

22 Sep '14

Hey all, Anybody want to write a blog post or two for the blog? I think having just short little ones about some new things in yt would be great. Like, a short one talking about new things in 3.0 for instance. Anybody interested? -Matt

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Issue #908: data_source.volume() still uses 2.x CellVolume field (yt_analysis/yt)
by John Wise 22 Sep '14

22 Sep '14

New issue 908: data_source.volume() still uses 2.x CellVolume field https://bitbucket.org/yt_analysis/yt/issue/908/data_sourcevolume-still-uses… John Wise: The `volume()` call in the `YTSelectionContainer3D` object still uses `CellVolume` to calculate the volume. This should be changed to `cell_volume`.

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GDF PR--call for some feedback
by John Zuhone 22 Sep '14

22 Sep '14

Hi all, I have a work-in-progress PR in the hopper regarding GDF reading and writing: https://bitbucket.org/yt_analysis/yt/pull-request/1001/wip-some-gdf-writing… What it does is implement direct writing of covering grids to GDF files (something I've been using in my research, to work with the resulting files directly in yt) and clobbering existing files with the same path if the user allows for it. However, when fiddling around with this I determined that it was necessary to make GDF more unit-aware. Ultimately, I determined that changes were needed that would break the standard that we had determined for the files (http://yt-project.org/gdf.txt). The two main changes are: 1) Remove "field_to_cgs", and allow the fields to be in whatever units we wish them to be in the file (which are specified as HDF5 attributes). 2) Add a new top-level group containing the information for "length","mass", and "time" units. These will be used when the file is opened up in yt to determine the units. Since (for now) we do automatic conversion to cgs, that is something that is still left unimplemented, but otherwise I think this is all to do for now. I'm writing the email in case anyone has any suggestions or objections to the format changes--particularly Jeff or Kacper. We'll obviously need to document them if they are accepted. Best, John -- John ZuHone Postdoctoral Researcher NASA/Goddard Space Flight Center jzuhone(a)gmail.com john.zuhone(a)nasa.gov

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Reviewers for PR 1186?
by Andrew Myers 21 Sep '14

21 Sep '14

Hi folks, Could I drum up a couple more reviewers for PR 1186? The guidelines require 3 approvers, and I'd like to get this merged because I have some unrelated changes I'd like to make soonish. Thanks, Andrew https://bitbucket.org/yt_analysis/yt/pull-request/1186/chombo-frontend-impr…

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soliciting for help with a possible Boston-based yt workshop
by John ZuHone 19 Sep '14

19 Sep '14

Hi developers, Well, I was only here in Cambridge for two weeks and someone already asked me if we could do a local yt workshop for users. They suggested that between CfA, MIT, and the other various institutions that there is probably a critical mass for a small workshop. I would be happy to organize and lead such a workshop, but it would be a lot easier on me if I had one or two others to help assist. This would be a small endeavor, and only local, but I was wondering if any of you might be potentially interested in coming up this way to help out. I cannot promise anything in the way of reimbursement at the outset, but I'm presuming so long as it's just one or two of you we can work something out easily. I am thinking December at the earliest, or maybe early next year. I know we are focused right now on the broader, more important workshop coming up at UIUC (yay, I get to go home!), but I thought I'd put this out there in case anyone is interested. Best, John Z

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Issue #907: changing units manually in FLASH datasets (yt_analysis/yt)
by Salvatore Cielo 19 Sep '14

19 Sep '14

New issue 907: changing units manually in FLASH datasets https://bitbucket.org/yt_analysis/yt/issue/907/changing-units-manually-in-f… Salvatore Cielo: Hello everyone, I am a new yt user; working with FLASH datafiles. FLASH files work smoothly in general, but the front-end seems to lack the possibility to change the unit system in reading, on the contrary of some other dataset (e.g. Athena) where one can specify units at load time. I need to specify a custom unit system; either at load time or later. I mean, I want yt to read the exact numbers on the file, but attach different physical units to them. My files may be a bit special under this aspect, but it's true that the FLASH front-end assumes cgs only. Under http://yt.readthedocs.org/en/latest/examining/supported_frontends_data.html, the user is warned that this will happen, but there's no solution or workaround proposed... I'd please like to know whether there's a way to change the units of a dataset, or to include the possibility of doing this manually in the front-end at load time. Thank you!

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Issue #906: Active Particle FieldNotFound (yt_analysis/yt)
by John Regan 19 Sep '14

19 Sep '14

New issue 906: Active Particle FieldNotFound https://bitbucket.org/yt_analysis/yt/issue/906/active-particle-fieldnotfound John Regan: I've added an ActiveParticle to Enzo which is created at a user appointed time. Running YT on the output before the particle is created causes YT to exit with the error yt.utilities.exceptions.YTFieldNotFound: Could not find field '('RadiationParticle', 'particle_velocity_z')'. Tunning YT on the outputs after the particle is created presents to problems. The problem can be recreated easily with the following script import yt # set up our namespace Filename = "/homeappl/home/regan/appl_taito/ENZO/3.0/RP-fork/enzo-3.0-rp/run/CosmologySimulation/AMRCosmology_RadiationParticle/RD0000/RD0000" ds = yt.load(Filename) ds.index.print_stats() The output (RD0000) can be found here. https://dl.dropboxusercontent.com/u/18978426/ActiveParticleRD0000.tgz Responsible: MatthewTurk

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Issue #905: Cannot create plots from a data source (yt_analysis/yt)
by Nathan Goldbaum 19 Sep '14

19 Sep '14

New issue 905: Cannot create plots from a data source https://bitbucket.org/yt_analysis/yt/issue/905/cannot-create-plots-from-a-d… Nathan Goldbaum: A field detection/generation issue is breaking `to_pw`: ``` #!python import yt ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') prj = ds.proj('density', 2) plot = prj.to_pw() ``` This raises the following traceback on the current tip of the yt branch: ``` #!python Traceback (most recent call last): File "test.py", line 4, in <module> plot = prj.to_pw() File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/construction_data_containers.py", line 389, in to_pw pw = self._get_pw(fields, center, width, origin, 'Projection') File "/Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.py", line 810, in _get_pw frb_generator=frb, plot_type=plot_type) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 618, in __init__ PlotWindow.__init__(self, *args, **kwargs) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 203, in __init__ self._set_window(bounds) # this automatically updates the data and plot File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_container.py", line 46, in newfunc args[0]._recreate_frb() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 254, in _recreate_frb self.frb._get_data_source_fields() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/fixed_resolution.py", line 143, in _get_data_source_fields if f not in exclude and f[0] not in self.data_source.ds.particle_types: TypeError: 'NoneType' object has no attribute '__getitem__' ```

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Issue #904: Reading in orion sink / star particle files is busted in yt-3.0 (yt_analysis/yt)
by Andrew Myers 19 Sep '14

19 Sep '14

New issue 904: Reading in orion sink / star particle files is busted in yt-3.0 https://bitbucket.org/yt_analysis/yt/issue/904/reading-in-orion-sink-star-p… Andrew Myers: This was reported via email by Stella Offner and Brandt Gaches. The code that reads them in needs to be updated to handle units. Also, the detection of particle fields got busted in some of the refactoring that went along with the transition from 2.X to 3.0. Responsible: atmyers

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