Mailman 3 May 2013 - yt-dev

Issue #577: VirialFilter fails if a profile has zeros in it. (yt_analysis/yt)
by Britton Smith May 24, 2013

May 24, 2013

New issue 577: VirialFilter fails if a profile has zeros in it. https://bitbucket.org/yt_analysis/yt/issue/577/virialfilter-fails-if-a-prof… Britton Smith: The virial does interpolation in log space to calculate values at r_200. If the profile has zeros in it, the interpolated values come out as NaN. Responsible: brittonsmith

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Issue #576: FLASH Halo Profiler dies on Dark_Matter_Density (yt_analysis/yt)
by Matthew Turk May 23, 2013

May 23, 2013

New issue 576: FLASH Halo Profiler dies on Dark_Matter_Density https://bitbucket.org/yt_analysis/yt/issue/576/flash-halo-profiler-dies-on Matthew Turk: The lack of Dark_Matter_Density in FLASH causes the HaloProfiler to die. http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-May/003152.h… Responsible: MatthewTurk

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(HaloProfiler) Best way to handle Dark_Matter_Density?
by Matthew Turk May 23, 2013

May 23, 2013

Hi all, This came up after a discussion on #yt; I've CC'd the person who brought this up. In the halo profiler, there's a list of standard fields. In this we have Dark_Matter_Density, which to my understanding is an Enzo-specific field. It's not the same as the CIC_Deposit3 (defined in yt) field that does a similar thing, but it's very similar. I am wondering what the best way to handle this, particularly since any frontend that wants to use the HaloProfiler will need this field unless … [View More]

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"faking" away variable-by-level refinement
by Chris Malone May 23, 2013

May 23, 2013

Hi all, I've been out of the yt-loop for awhile, but am now getting back into the game. In particular I work with the BoxLib-based codes, Maestro and Castro. I'm glad Matt has taken the time to consolidate the BoxLib frontends - this is something I've wanted to do for some time! One issue that has come up is that (at least) Castro supports jumps in refinement that can vary between levels. In other words, Level 1 might be twice as refined as Level 0, but Level 2 might be four times as … [View More]

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Issue #575: Adding a field after parameter file instantiation results in bad generation (yt_analysis/yt)
by Matthew Turk May 22, 2013

May 22, 2013

New issue 575: Adding a field after parameter file instantiation results in bad generation https://bitbucket.org/yt_analysis/yt/issue/575/adding-a-field-after-paramet… Matthew Turk: If a field is added after a parameter file is loaded, we end up with a bad state in `pf.field_dependencies` which then causes `_identify_dependencies` to continue and not provide any dependencies. This then causes `_read_fluid_fields` to return not enough data, and then a `GenerationInProgress` gets thrown from … [View More]

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Issue #574: Array index error in light ray generator (yt_analysis/yt)
by Britton Smith May 22, 2013

May 22, 2013

New issue 574: Array index error in light ray generator https://bitbucket.org/yt_analysis/yt/issue/574/array-index-error-in-light-r… Britton Smith: Occasionally, there is an array index error in the light rays during the step where the cells with zero path length are being removed around line 408 of light_ray.py. This appears to be because the dictionary holding all of the field data has multiple entries for a few fields, so they get altered more than once. Responsible: brittonsmith

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Issue #573: The install script breaks if CC is set to a full path on OS X (yt_analysis/yt)
by Nathan Goldbaum May 21, 2013

May 21, 2013

New issue 573: The install script breaks if CC is set to a full path on OS X https://bitbucket.org/yt_analysis/yt/issue/573/the-install-script-breaks-if… Nathan Goldbaum: If someone sets CC to be a full path: ``` #!bash export CC=/usr/bin/gcc ``` The install script will fail due to an invocation of sed: ``` #!bash Installing BZLIB sed: 1: "s/CC=gcc/CC=/usr/bin/gcc/ ": bad flag in substitute command: 'u' ******************************************** FAILURE REPORT: ***************… [View More]

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Kill logging in the notebook?
by Nathan Goldbaum May 21, 2013

May 21, 2013

Hi all, I have a quick request for feedback about a change to the way yt.imods works. I'm of the opinion that the logging, while useful and nice when calling yt from a script or an IPython prompt, makes for a bad UI experience from inside the notebook. The logs are sent to stderr, so they show up in the notebook output in a scary looking red box. Worse, vertical space is at a premium on the widescreen displays that most of us use, and the logging output tends to push the results we … [View More]

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Issue #572: Plot window plots of arrays that contain data filled with zeros will sometimes fail. (yt_analysis/yt)
by Nathan Goldbaum May 21, 2013

May 21, 2013

New issue 572: Plot window plots of arrays that contain data filled with zeros will sometimes fail. https://bitbucket.org/yt_analysis/yt/issue/572/plot-window-plots-of-arrays-… Nathan Goldbaum: This multispecies enzo dataset is initialized to contain only ionized hydrogen, so the `HI_Density` field is zero everywhere. Since this field is set to have a logarithmic colorbar by default, if I try to plot the field, the plotting code crashes: ``` #!python from yt.mods import * pf = load('… [View More]DD0000/DD0000') slc = SlicePlot(pf, 0, 'HI_Density') ``` ``` #!python Traceback (most recent call last): File "test.py", line 3, in <module> slc = SlicePlot(pf,0,'HI_Density') File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 1222, in __init__ PWViewerMPL.__init__(self, slc, bounds, origin=origin, fontsize=fontsize) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 781, in __init__ PWViewer.__init__(self, *args, **kwargs) File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 605, in __init__ if setup: self._setup_plots() File "/Users/goldbaum/Documents/yt-hg/yt/visualization/plot_window.py", line 890, in _setup_plots self.plots[f].image, cax = self.plots[f].cax) File "/usr/local/lib/python2.7/site-packages/matplotlib/figure.py", line 1394, in colorbar cb = cbar.colorbar_factory(cax, mappable, **kw) File "/usr/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory cb = Colorbar(cax, mappable, **kwargs) File "/usr/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 854, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/usr/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 298, in __init__ self.draw_all() File "/usr/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 319, in draw_all self._process_values() File "/usr/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 632, in _process_values b = self.norm.inverse(self._uniform_y(self.cmap.N+1)) File "/usr/local/lib/python2.7/site-packages/matplotlib/colors.py", line 982, in inverse return vmin * ma.power((vmax / vmin), val) File "/usr/local/lib/python2.7/site-packages/numpy/ma/core.py", line 3648, in __mul__ return multiply(self, other) File "/usr/local/lib/python2.7/site-packages/numpy/ma/core.py", line 941, in __call__ if m: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ``` This could be fixed by switching to a linear colorbar inline. Responsible: ngoldbaum [View Less]

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Issue #571: HaloFinder.write_out() cannot save file to current directory (yt_analysis/yt)
by Kacper Kowalik May 19, 2013

May 19, 2013

New issue 571: HaloFinder.write_out() cannot save file to current directory https://bitbucket.org/yt_analysis/yt/issue/571/halofinderwrite_out-cannot-s… Kacper Kowalik: Revision 40beb2f causes following script (part of yt-doc): ``` #!python from yt.mods import * pf = load("Enzo_64/DD0043/data0043") halos = HaloFinder(pf) halos.write_out("%s_halos.txt" % pf) ``` to fail with: ``` #!text File "/tmp/jenkins/workspace/yt-docs/source/cookbook/halo_finding.py", line 10, in <module> … [View More]

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