Mailman 3 April 2013 - yt-dev

[yt_analysis/yt] Document the field_cuts keyword arg for projections. (issue #555)
by Britton Smith 23 Apr '13

23 Apr '13

New issue 555: Document the field_cuts keyword arg for projections. https://bitbucket.org/yt_analysis/yt/issue/555/document-the-field_cuts-keyw… Britton Smith: Some discussion should be added to the field_cuts section in analyzing/objects section that discusses this specific use with projections.

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[yt_analysis/yt] Document cosmology units (issue #554)
by Nathan Goldbaum 22 Apr '13

22 Apr '13

New issue 554: Document cosmology units https://bitbucket.org/yt_analysis/yt/issue/554/document-cosmology-units Nathan Goldbaum: There should be an overview of yt's capabilities for handling cosmology simulations. In particular, the 'cm' and 'hcm' patterns for comoving units should be documented.

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Exporting to radmc3d
by Andrew Myers 22 Apr '13

22 Apr '13

Hi Folks, radmc3d <http://www.ita.uni-heidelberg.de/~dullemond/software/radmc-3d/> is a Monte Carlo radiative transfer code that can produce spectra and images for dust continuum and line radiation. I've written some code to save out a yt dataset into the format it uses for its AMR input files. It needs some cleaning up and documentation, but if this is something other people are interested in, I'd be happy to try to add it to yt code base. In principle, this would let any code with a yt frontend interface with radmc3d without too much hassle. -Andrew

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Re: [yt-dev] yt Strategy Meeting Tuesday the 23rd: Change of time!
by Matthew Turk 22 Apr '13

22 Apr '13

Hi all, A number of people have written to me off list requesting a change, so this will instead be on Tuesday the 23rd at 1PM Eastern. I've created an event on Google Plus on the yt page. I've set it to public, because we don't have everyone in circles yet on there. Here's the event page: https://plus.google.com/events/cr7ro5oulb5unkr3lfe80njo5o0 -Matt On Sat, Apr 13, 2013 at 10:08 AM, Matthew Turk <matthewturk(a)gmail.com> wrote: > Hi all, > > I'd like to call a brief, approximately one hour, strategy meeting on > Monday, April 22nd at 3PM Eastern. This will cover where yt is at, > where we can go, and how things are progressing. Some of this will be > dedicated to progress updates (from me and others) as well as > soliciting feedback on a number of things. Many other projects -- > notably Cactus -- do these on a fixed schedule, so based on the > success/failure of this one we can consider having them > semi-regularly. > > The agenda I would like to cover will include: > > * yt 3.0 status, including near/long term plans for development and > support for non-grid codes > * Rundown of all YTEPs accepted and outstanding > * yt's "presence" on the web > * 3.0 paper > > I will also be soliciting feedback in roundtable style on: > > * How are we doing? > * How is the procedure for code contributions working? > * How is the yt "infrastructure" meeting people's needs? (Mailing > lists, Bitbucket, etc) > * Where are energies being spent that could be better spent elsewhere? > > If you have either agenda items or discussion items, please reply to > this email and suggest them. > > I think having a large presence at this meeting would be very useful, > so if you are able to make it, please try to do so. It'll be held as > a google hangout, and I'll send details here when it starts up. If > there's a pressing need to reschedule, please write in reply to this > email. > > Thanks, and looking forward to seeing you there, > > Matt

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[yt_analysis/yt] _identify_base_chunk for Octree codes should not pre-allocate a mask (issue #553)
by Matthew Turk 18 Apr '13

18 Apr '13

New issue 553: _identify_base_chunk for Octree codes should not pre-allocate a mask https://bitbucket.org/yt_analysis/yt/issue/553/_identify_base_chunk-for-oct… Matthew Turk: The mask for child octs should not be allocated during the course of `_identify_base_chunk` if it can at all be avoided. This is costly. Responsible: MatthewTurk

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Make DomainSubsets a subclass of YTSelectionContainer?
by Matthew Turk 17 Apr '13

17 Apr '13

Hi all, Today in IRC, Chris and I went back and forth on the particle deposition stuff in advance of the meeting next week. My task right now is to come up with spatial field chunking for Octs in a consistent way; of course I'll write this up into the extant YTEP, which will allow for feedback particularly from ARTIO, ART and RAMSES folks, but as a quick first pass I was wondering what everyone thought of: 1) Unifying DomainSubsets into a single object with subclasses 2) Making that new base class a subclass, itself, of YTSelectionContainer This would mean that this new base class would be very similar to the GridPatch object -- which it already is -- and would implement, most crucially, the __getitem__ accessor pattern. This would return a 2x2x2xNoct field. [+-][01]? Specifically, Doug, Chris, and SamL? Sidenote: I discovered that we will not have to rewrite spatial fields that currently work for grids; my understanding of the numpy broadcasting system was not complete, and I didn't realize that this script does *exactly what I want it to. http://paste.yt-project.org/show/3391/ This means that our Oct spatial fields will be (2+NGZ*2, 2+NGZ*2, 2+NGZ*2, NOCT) shaped.

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[yt_analysis/yt] cut_region doesn't work in 3.0 (issue #552)
by Nathan Goldbaum 17 Apr '13

17 Apr '13

New issue 552: cut_region doesn't work in 3.0 https://bitbucket.org/yt_analysis/yt/issue/552/cut_region-doesnt-work-in-30 Nathan Goldbaum: It seems that subselecting on data objects using field cuts hasn't been implemented in 3.0. ``` #!python from yt.mods import * pf = load('DD0000/DD0000') dd = pf.h.all_data() lt = dd.cut_region("grid['Temperature'] < 1e5") lt['CellMassMsun'].sum() ``` ``` #!python traceback Traceback (most recent call last): File "test2.py", line 8, in <module> lt['CellMassMsun'].sum() File "/home/goldbaum/yt-3.0/yt/data_objects/data_containers.py", line 200, in __getitem__ self.get_data(f) File "/home/goldbaum/yt-3.0/yt/data_objects/data_containers.py", line 470, in get_data self.hierarchy._identify_base_chunk(self) File "/home/goldbaum/yt-3.0/yt/geometry/grid_geometry_handler.py", line 237, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/home/goldbaum/yt-3.0/yt/data_objects/data_containers.py", line 441, in selector raise YTDataSelectorNotImplemented(self._type_name) yt.utilities.exceptions.YTDataSelectorNotImplemented: Data selector 'cut_region' not implemented. ```

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[yt_analysis/yt] Ellipsoidal particle IO does not work (issue #551)
by Matthew Turk 16 Apr '13

16 Apr '13

New issue 551: Ellipsoidal particle IO does not work https://bitbucket.org/yt_analysis/yt/issue/551/ellipsoidal-particle-io-does… Matthew Turk: This is because of a bug in the ParticleIOHandler that we fall back on when we define a method of ParticleIO (only Enzo) and do not for a 3D data object (only ellipsoid.)

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YTEP-0013: First Class Deposited Particle Fields
by Christopher Moody 15 Apr '13

15 Apr '13

Hi all, I've issued a PR for YTEP-0013, which tries to promote deposited particle fields to being a first-class field type. This extends the (field_type, field_name) syntax, adds a new concept of the 'deposit' field_type. If you're at all interested in how particles are treated in yt, I'd encourage you to look at the PR and comment! https://bitbucket.org/yt_analysis/ytep/pull-request/15/ytep-0013-first-clas… Thanks! chris

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[yt_analysis/yt] Native gdf files fail with SlicePlot (issue #550)
by Kacper Kowalik 15 Apr '13

15 Apr '13

New issue 550: Native gdf files fail with SlicePlot https://bitbucket.org/yt_analysis/yt/issue/550/native-gdf-files-fail-with-s… Kacper Kowalik: Following code: ``` #!python from yt.mods \ import load, SlicePlot from yt.utilities.grid_data_format.writer \ import write_to_gdf pf = load('yt/tests/DD0010/moving7_0010') write_to_gdf(pf, 'moving7_0010.gdf') del pf pf = load('moving7_0010.gdf') slc = SlicePlot(pf, 'z', 'Density') slc.save() ``` yields ``` #!bash File "foobar.py", line 14, in <module> slc = SlicePlot(pf, 'z', 'Density') File "/home/xarth/codes/yt/yt/visualization/plot_window.py", line 1143, in __init__ PWViewerMPL.__init__(self, slc, bounds, origin=origin, fontsize=fontsize) File "/home/xarth/codes/yt/yt/visualization/plot_window.py", line 743, in __init__ PWViewer.__init__(self, *args, **kwargs) File "/home/xarth/codes/yt/yt/visualization/plot_window.py", line 568, in __init__ if setup: self._setup_plots() File "/home/xarth/codes/yt/yt/visualization/plot_window.py", line 877, in _setup_plots parser.parse(colorbar_label) File "/usr/lib64/python2.7/site-packages/matplotlib/mathtext.py", line 3010, in parse box = self._parser.parse(s, font_output, fontsize, dpi) File "/usr/lib64/python2.7/site-packages/matplotlib/mathtext.py", line 2344, in parse str(err)])) ValueError: \/\/(\) ^ Unknown symbol: \ (at char 5), (line:1, col:6) ```

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