Mailman 3 March 2014 - yt-dev

Issue #798: PhasePlot does not support annotate_line (yt_analysis/yt)
by Stephanie Tonnesen March 5, 2014

March 5, 2014

New issue 798: PhasePlot does not support annotate_line https://bitbucket.org/yt_analysis/yt/issue/798/phaseplot-does-not-support-a… Stephanie Tonnesen: AttributeError: 'PhasePlot' object has no attribute 'annotate_line' in Version 2.7-dev that I updated March 5.

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Question about vorticity and divergence plots
by 吳佳鴻 March 5, 2014

March 5, 2014

Dear all, I’m new to YT. I encountered a problem when trying to plot the divergence and vorticity of a velocity field with an octree data structure similar to FLASH. I put a cylindrically symmetric velocity field into YT. So far I could get Velocity Magnitude Plot correctly and the Velocity vector looks also fine (see the attachment). However, the VorticityMagnitude and DivV plots have a offset toward the top right corner. I was wondering where I did it wrong. Any suggestion will be … [View More]

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Issue #797: Handling cell_volume in 1D and 2D cartesian (yt_analysis/yt)
by John ZuHone March 5, 2014

March 5, 2014

New issue 797: Handling cell_volume in 1D and 2D cartesian https://bitbucket.org/yt_analysis/yt/issue/797/handling-cell_volume-in-1d-a… John ZuHone: `cell_volume` is ill-defined for 1D and 2D cartesian data because it is still given in terms of length**3, even though the unused dimensions are meaningless. What we have done is set the `domain_width` to unity in these cases, but with the unit refactor I think this issue ought to be revisited. That said, I'm not sure what to do about it. Responsible: jzuhone

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Issue #796: Clump finding fails for uniform grid data (yt_analysis/yt)
by Kacper Kowalik March 4, 2014

March 4, 2014

New issue 796: Clump finding fails for uniform grid data https://bitbucket.org/yt_analysis/yt/issue/796/clump-finding-fails-for-unif… Kacper Kowalik: Following script: ``` #!python import numpy as np from yt.frontends.stream.api import load_uniform_grid from yt.mods import amods def gaussian(size, sigma): il = size // 2 x, y, z = np.mgrid[-il + 1:il + 1, -il + 1:il + 1, -il + 1:il + 1] sg2 = 2.0 * sigma ** 2 return np.exp(-(x ** 2 + y ** 2 + z ** 2) / sg2) / (np.pi * sg2) … [View More]def diag_shift(tab, n): a = np.roll(tab, int(n), axis=0) a = np.roll(a, int(n), axis=1) return np.roll(a, int(n), axis=2) N = 64 dims = [N, N, N] dens = np.ones(dims) \ + 50.0 * diag_shift(gaussian(N, 5.0), -12) \ + 10.0 * diag_shift(gaussian(N, 3.0), 10) data = dict(Density=dens) bbox = np.array([[-1.0, 1.0], [-1.0, 1.0], [-1.0, 1.0]]) pf = load_uniform_grid(data, dens.shape, 1.0, bbox=bbox, nprocs=2) field = "Density" step = 4 data_source = pf.h.all_data() c_min = 10 ** np.floor(np.log10(data_source[field]).min()) c_max = 10 ** np.floor(np.log10(data_source[field]).max() + 1) function = 'self.data["%s"].size > 20' % field master_clump = amods.level_sets.Clump(data_source, None, field, function=function) master_clump.clear_clump_info() master_clump.add_info_item('self.data["%s"].size' % field, '"Cells: %d" % value') master_clump.add_info_item( '(self.data["%s"] * self.data["CellVolume"]).sum()' % field, '"Mass: %e g" % value') master_clump.add_info_item( 'self.data["%s"].mean()' % field, '"Mean density: %e" % value') amods.level_sets.find_clumps(master_clump, c_min, c_max, step) ``` fails with ``` #!bash P000 yt : [INFO ] 2014-03-04 18:27:59,250 Parameters: current_time = 0.0 P000 yt : [INFO ] 2014-03-04 18:27:59,250 Parameters: domain_dimensions = [64 64 64] P000 yt : [INFO ] 2014-03-04 18:27:59,251 Parameters: domain_left_edge = [-1. -1. -1.] P000 yt : [INFO ] 2014-03-04 18:27:59,252 Parameters: domain_right_edge = [ 1. 1. 1.] P000 yt : [INFO ] 2014-03-04 18:27:59,252 Parameters: cosmological_simulation = 0.0 Finding clumps: min: 1.000000e+00, max: 1.000000e+01, step: 4.000000 P000 yt : [INFO ] 2014-03-04 18:27:59,933 Linking node (2) contours. Couldn't find 4607182418800017408 Inspected 2 Exception RuntimeError: RuntimeError() in 'yt.utilities.lib.ContourFinding.construct_boundary_relationships' ignored P000 yt : [INFO ] 2014-03-04 18:28:00,008 Linked. P000 yt : [INFO ] 2014-03-04 18:28:00,008 Starting 'Updating joins ... ' P000 yt : [INFO ] 2014-03-04 18:28:00,026 Finishing 'Updating joins ... ' Investigating 2 children. Finding clumps: min: 4.000000e+00, max: 1.000000e+01, step: 4.000000 Traceback (most recent call last): File "clumps_issue.py", line 49, in <module> amods.level_sets.find_clumps(master_clump, c_min, c_max, step) File "yt/analysis_modules/level_sets/clump_handling.py", line 180, in find_clumps find_clumps(child, min_val*d_clump, max_val, d_clump) File "yt/analysis_modules/level_sets/clump_handling.py", line 171, in find_clumps clump.find_children(min_val) File "yt/analysis_modules/level_sets/clump_handling.py", line 110, in find_children nj, cids = identify_contours(self.data, self.field, min_val, max_val) File "yt/analysis_modules/level_sets/contour_finder.py", line 31, in identify_contours for (g, node, (sl, dims, gi)) in data_source.tiles.slice_traverse(): File "yt/data_objects/data_containers.py", line 442, in tiles self._tree = AMRKDTree(self.pf, data_source=self) File "yt/utilities/amr_kdtree/amr_kdtree.py", line 162, in __init__ data_source=data_source) File "yt/utilities/amr_kdtree/amr_kdtree.py", line 69, in __init__ self.build() File "yt/utilities/amr_kdtree/amr_kdtree.py", line 83, in build grids = np.array([b for b, mask in self.data_source.blocks if b.Level == lvl]) File "yt/data_objects/data_containers.py", line 451, in blocks o = self._current_chunk.objs[0] AttributeError: 'NoneType' object has no attribute 'objs' ``` using `yt-3.0` rev `3e8b733c9ee9` [View Less]

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ITER Fly-Through
by Anthony Scopatz March 1, 2014

March 1, 2014

Hello All, Here are the results of the hack session with Matt Turk, Elliott Biondo, Patrick Shriwise, Matt Gidden, and myself yesterday. I would call this a success :). Be Well Anthony 1. http://nbviewer.ipython.org/github/pyne/sandbox/blob/master/iter-surfaces.i… PS 1008 frames / 24 fps = 42 sec. Just saying.

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Fwd: [Discuss] second call: 21st Century science
by Matthew Turk March 1, 2014

March 1, 2014

I imagine someone here might have something to contribute. ---------- Forwarded message ---------- From: Greg Wilson <gvwilson(a)software-carpentry.org> Date: Sat, Mar 1, 2014 at 9:25 AM Subject: [Discuss] second call: 21st Century science To: Software Carpentry Discussion <discuss(a)lists.software-carpentry.org> Hi, I asked a few weeks ago for examples of 21st Century science to include on our web site: > I'd like to put together a page on the web site to show people how we … [View More]

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Issue #795: ART particle data file recognition (yt_analysis/yt)
by karraki March 1, 2014

March 1, 2014

New issue 795: ART particle data file recognition https://bitbucket.org/yt_analysis/yt/issue/795/art-particle-data-file-recog… karraki: yt is unable to automatically locate the particle data file when certain ART files are loaded. For instance: ``` #!python pf = load('10MpcBox_HartGal_csf_a0.500.d') yt : [INFO ] 2014-02-28 15:07:24,747 discovered particle_data:/hyades/karraki/yt/scripts/10MpcBox_HartGal_csf_a0.500.d ``` This only occurs with Sebastian's output files not Daniel's … [View More]

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2.6.2 on Thursday
by Matthew Turk March 1, 2014

March 1, 2014

Hi all, We've had a couple critical bug fixes go in to the mainline 2.x branch lately, and we're also slightly overdue for a 2.6.2. So I would like to cut a release on Thursday. If there are any objections, let me know, otherwise I'll proceed with merging into stable, tagging, and uploading to pypi. John ZuHone pointed out that with Kacper's fixes to the packaging and his fixes to various imports and whatnot we ought to keep to this schedule; I've let it slip a little. -Matt

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