Mailman 3 September 2016 - yt-dev

SPH Smoothing Formulation?
by Cameron Hummels 09 Sep '16

09 Sep '16

Hey everyone, Britton, Devin, and I are writing up the Trident method paper, and we wanted to be explicit about how exactly yt deposits SPH field quantities on to an octree for particle-based fields. Are there any formal equations for this written down anywhere? I realize SPH support was added since the first yt method paper, so it isn't in there, and I cannot seem to find anything in the docs. I wonder if anyone has anything written down for this or if I'm missing it somewhere? Thanks! Cameron -- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org

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Issue #1275: Doc notebooks are not properly evaluated (yt_analysis/yt)
by Kacper Kowalik 07 Sep '16

07 Sep '16

New issue 1275: Doc notebooks are not properly evaluated https://bitbucket.org/yt_analysis/yt/issues/1275/doc-notebooks-are-not-prop… Kacper Kowalik: There's no difference between ["raw"](http://yt-project.org/docs/dev/analyzing/analysis_modules/Particle_Trajectories.ipynb) and ["evaluated"](http://yt-project.org/docs/dev/analyzing/analysis_modules/Particle_Trajectories_evaluated.ipynb)

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Issue #1274: RAMSES temperature units wrong (yt_analysis/yt)
by Pawel Biernacki 07 Sep '16

07 Sep '16

New issue 1274: RAMSES temperature units wrong https://bitbucket.org/yt_analysis/yt/issues/1274/ramses-temperature-units-w… Pawel Biernacki: Hi! I tried newest pip yt today after a long break and plotted RAMSES isolated galaxy. The temperatures I got were ~1e10 K, which is incorrect. I think in the conversion of temperature you forgot to check the boxsize (in my case it was 60. in code units), so I'd see the problem in this.

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Issue #1273: Mesh line annotations are wrong when the slice exactly intersects element boundaries. (yt_analysis/yt)
by Anonymous 06 Sep '16

06 Sep '16

New issue 1273: Mesh line annotations are wrong when the slice exactly intersects element boundaries. https://bitbucket.org/yt_analysis/yt/issues/1273/mesh-line-annotations-are-… Anonymous: Thanks to @xarthisius for tracking this down. Responsible: atmyers

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PR review hangout
by Nathan Goldbaum 06 Sep '16

06 Sep '16

Hi all, I've created an event for the PR review hangout tomorrow at 1:00 PM CDT: https://plus.google.com/u/0/b/107728486871834552760/events/cvcf3ka2g20upmvp… -Nathan

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Issue #1272: Error when using load_octree (yt_analysis/yt)
by Anonymous 04 Sep '16

04 Sep '16

New issue 1272: Error when using load_octree https://bitbucket.org/yt_analysis/yt/issues/1272/error-when-using-load_octr… Anonymous: The following code: ``` #!python import numpy as np from yt.mods import load_octree, ProjectionPlot octree_mask = np.array([8,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0], dtype=np.uint8) quantities = {} quantities[('gas', 'density')] = np.ones((22,1), dtype=float) bbox = np.array([[-10., 10.], [-10., 10.], [-10., 10.]]) spf = load_octree(octree_mask=octree_mask, data=quantities, bbox=bbox, over_refine_factor=0, partial_coverage=0) p = ProjectionPlot(spf, 'x', ['density'], center='c', origin='native') ``` produces the following error: ``` yt : [INFO ] 2016-09-04 22:19:26,815 Parameters: current_time = 0.0 yt : [INFO ] 2016-09-04 22:19:26,815 Parameters: domain_dimensions = [1 1 1] yt : [INFO ] 2016-09-04 22:19:26,816 Parameters: domain_left_edge = [-10. -10. -10.] yt : [INFO ] 2016-09-04 22:19:26,817 Parameters: domain_right_edge = [ 10. 10. 10.] yt : [INFO ] 2016-09-04 22:19:26,817 Parameters: cosmological_simulation = 0.0 Traceback (most recent call last): File "debug.py", line 18, in <module> p = ProjectionPlot(spf, 'x', ['density'], center='c', origin='native') File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/visualization/plot_window.py", line 1433, in __init__ max_level=max_level) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 262, in __init__ self.get_data(field) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 336, in get_data self._handle_chunk(chunk, fields, tree) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/data_objects/construction_data_containers.py", line 436, in _handle_chunk d = chunk[field] * dl File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/data_objects/data_containers.py", line 1178, in get_data fluids, self, self._current_chunk) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/geometry/geometry_handler.py", line 245, in _read_fluid_fields chunk_size) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/frontends/stream/io.py", line 252, in _read_fluid_selection subset.fill(field_vals, rv, selector, ind) File "/Users/tom/miniconda3/envs/dev35/lib/python3.5/site-packages/yt/frontends/stream/data_structures.py", line 1402, in fill selector, self.domain_id, cell_count) File "yt/geometry/oct_container.pyx", line 775, in yt.geometry.oct_container.OctreeContainer.file_index_octs (yt/geometry/oct_container.c:13230) ValueError: Buffer dtype mismatch, expected 'uint8_t' but got 'long' ``` I'm using yt 3.3.1 from conda-forge and Python 3.5. This works correctly with yt 3.2.3 from conda-forge though, so I think it must be a bug in the 3.3 series?

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Issue #1271: Derived fields that return data with incorrect shape should raise errors (yt_analysis/yt)
by Nathan Goldbaum 02 Sep '16

02 Sep '16

New issue 1271: Derived fields that return data with incorrect shape should raise errors https://bitbucket.org/yt_analysis/yt/issues/1271/derived-fields-that-return… Nathan Goldbaum: Here's a test script that illustrates the problem: ``` import numpy as np import yt @yt.derived_field(name='wrong_field', units='') def wrong_field(field, data): return np.array([1, 2, 3]) ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') ad = ds.all_data() ad['wrong_field'] ``` On my machine, this prints: ``` YTArray([1, 2, 3]) (dimensionless) ``` The fact that this works without erroring out right now leads to broknness later and user confusion. See Issue #1270. Responsible: ngoldbaum

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Issue #1270: unable to plot created field (yt_analysis/yt)
by Rajika Kuruwita 01 Sep '16

01 Sep '16

New issue 1270: unable to plot created field https://bitbucket.org/yt_analysis/yt/issues/1270/unable-to-plot-created-fie… Rajika Kuruwita: Hi there, I have created some fields. It is able to plot some but others (particularly my Enclosed mass field and every other field that uses that field) cannot be plotted. When I try to use Sliceplot the warning "Plot image for field ('gas', 'Enclosed_Mass') has zero dynamic range. Min = Max = 0.000000.". However, when the field is retrieved using dd['Enclosed_Mass'], it is not all zero, in fact min=6.01427540665e+32 g and max=2.11538515805e+33 g. This field is not created in the conventional way, with one to one matrix math, and it is a bit slow to calculate because I used radial bins to approximate the value. But I think the main issue is that, the field is non-zero everywhere, but Sliceplot is unable to plot the field or other fiends that use it.

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