Mailman 3 March 2013 - yt-dev

NumberDensity in clumps and on FLASH data
by Matthew Turk July 10, 2013

July 10, 2013

Hi all, Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email: "Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset." The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data. I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas? -Matt

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YTEP-0012: Halos
by Matthew Turk April 1, 2013

April 1, 2013

Hi all, Britton issued a pull request for YTEP-0012, which covers halo finding, merger trees, and halo profiling. https://bitbucket.org/yt_analysis/ytep/pull-request/14/ytep-12-halo-analysi… I'm going to be leaving comments on it today, but if you are at all remotely interested in this functionality, I'd encourage you to submit feedback on it. -Matt

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Release of yt-2.5.1
by Matthew Turk March 31, 2013

March 31, 2013

Hi all, We're proud to release yt version 2.5.1. This is a scheduled point release that includes all bug fixes identified and fixed since the release of 2.5 on March 1. Major changes include: * The addition of a frontend for the Pluto code (Andrew Myers) * The addition of an OBJ exporter to enable transparent and multi-surface exports of surfaces to Blender and Sketchfab (Jill Naiman) There have also been a number of minor bugs fixed in this release. Some highlights: * load_uniform_grid can now decompose dims >= 1024. (#537) * Axis unit setting works correctly for unit names (#534) * ThermalEnergy is now calculated correctly for Enzo MHD simulations (#535) * Radius fields had an asymmetry in periodicity calculation (#531) * Boolean regions can now be pickled (#517) If you are using the stable branch of yt from an installation script, you can upgrade using "yt update". If you are using the development branch, you may already have these fixes. An installation-ready tarball with generated C code (i.e., no Cython) has been uploaded to the Python Package Index (PyPI). Thanks very much, Matt, on behalf of the yt development team

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[yt_analysis/yt] Create additional 'Version' values wrt YTEP-0008 (issue #538)
by Kacper Kowalik March 27, 2013

March 27, 2013

New issue 538: Create additional 'Version' values wrt YTEP-0008 https://bitbucket.org/yt_analysis/yt/issue/538/create-additional-version-va… Kacper Kowalik: We're missing a few keywords in "version" field. For this week at least "2.5.1" would come handy. Responsible: MatthewTurk -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] get_psize in load_uniform_grid breaks (issue #537)
by Matthew Turk March 26, 2013

March 26, 2013

New issue 537: get_psize in load_uniform_grid breaks https://bitbucket.org/yt_analysis/yt/issue/537/get_psize-in-load_uniform_gr… Matthew Turk: ``` #!python d = np.zeros((1024,1024,1024)) pf = load_uniform_grid({"Perturbation": d}, (1024,1024,1024), 100.0, bbox = np.array( [[mi, ma], [mi, ma], [mi, ma]] ), nprocs = 32) pf.h.print_stats() ``` This code (or switching to nprocs 8 or even 256) breaks with: ``` Traceback (most recent call last): File "convert.py", line 21, in <module> nprocs = 32) File "/home/mturk/yt/yt/yt/frontends/stream/data_structures.py", line 479, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) File "/home/mturk/yt/yt/yt/utilities/decompose.py", line 136, in get_psize return p_size UnboundLocalError: local variable 'p_size' referenced before assignment ``` Responsible: xarthisius -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] Cannot set the color via set_font (issue #536)
by Nathan Goldbaum March 26, 2013

March 26, 2013

New issue 536: Cannot set the color via set_font https://bitbucket.org/yt_analysis/yt/issue/536/cannot-set-the-color-via-set… Nathan Goldbaum: We should try to pop `color` or `colors` off of the font_dict before passing it to `FontProperties`. Responsible: ngoldbaum -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] Thermal Energy is incorrectly computed for enzo data with MHD and without DualEnergy (issue #535)
by J.S. Oishi March 25, 2013

March 25, 2013

New issue 535: Thermal Energy is incorrectly computed for enzo data with MHD and without DualEnergy https://bitbucket.org/yt_analysis/yt/issue/535/thermal-energy-is-incorrectl… J.S. Oishi: For enzo, in order to properly compute ThermalEnergy when MHD is on, one needs to subtract MagneticEnergy from TotalEnergy as wel las 0.5*v^2. This is only an issue if DualEnergy is off, since if it is on, ThermalEnergy is directly computed by Enzo. Responsible: jsoishi -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] Enzo-3.0 datasets that do not contain active particles cannot be read in. (issue #533)
by Nathan Goldbaum March 19, 2013

March 19, 2013

--- you can reply above this line --- New issue 533: Enzo-3.0 datasets that do not contain active particles cannot be read in. https://bitbucket.org/yt_analysis/yt/issue/533/enzo-30-datasets-that-do-not… Nathan Goldbaum: Enzo-3.0 datasets that do not contain active particles do not have an AppendActiveParticleType entry in the parameter file (and they shouldn't, I think). This breaks the enzo frontend since it assumes all 3.0 datasets contain such a key. Here's a traceback that exhibits this behavior: http://paste.yt-project.org/show/3270/ I can make this dataset available if it will be useful for debugging. -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] CIC deposited enzo fields are broken in 3.0 (issue #532)
by Nathan Goldbaum March 19, 2013

March 19, 2013

--- you can reply above this line --- New issue 532: CIC deposited enzo fields are broken in 3.0 https://bitbucket.org/yt_analysis/yt/issue/532/cic-deposited-enzo-fields-ar… Nathan Goldbaum: Fields like dm_density require a pass through CICDeposit_3, which seems to have a different signature in 3.0 compared to 2.X. Here's a traceback: http://paste.yt-project.org/show/3268/ The same command runs as expected in 2.6dev. -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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[yt_analysis/yt] "RadiusCode" field is ill-defined for periodic domains (issue #531)
by Kacper Kowalik March 19, 2013

March 19, 2013

--- you can reply above this line --- New issue 531: "RadiusCode" field is ill-defined for periodic domains https://bitbucket.org/yt_analysis/yt/issue/531/radiuscode-field-is-ill-defi… Kacper Kowalik: As per ml [thread](http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-Marc… following script: ``` #!python from yt.mods import * from yt.testing import * from yt.data_objects.universal_fields import get_radius from yt.data_objects.field_info_container import ValidateParameter @derived_field(name="invrad", validators = [ValidateParameter("center")]) def _invrad(field, data): data.set_field_parameter("center", [1.0, 1.0, 1.0]) return 1.0/data["RadiusCode"] pf = fake_random_pf(64) sp = pf.h.sphere([1.0, 1.0, 1.0], 0.25) r = get_radius(sp, "") if hasattr(sp, "size"): v = 3 p1 = pf.h.proj("invrad", 0, data_source = sp, style="mip") p2 = pf.h.proj("Density", 0, data_source = sp) else: v = 2 p1 = pf.h.proj(0, "invrad", source = sp, proj_style="mip") p2 = pf.h.proj(0, "Density", source = sp) pw1 = p1.to_pw() pw1.save("yt_v%s" % v) pw2 = p2.to_pw() pw2.set_zlim("Density", 0, 0.32) pw2.save("yt_v%s" % v) ``` produces ![Bad Density](http://i.imgur.com/mdmJqw6.png) ![Bad invrad](http://i.imgur.com/XmBmHZw.png) while it should yield ![Good Density](http://i.imgur.com/nUffCp2.png) ![Good invrad](http://i.imgur.com/FPISsvy.png) -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

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