[yt-users] Off Axis Projection Box size error

[Nathan Goldbaum]

The easiest way to workaround this issue is to do:

ds.periodicity = (True, True, True)

The issue you're running into always happens no matter what you choose for
the width because of the use of an all_data() data object internally, which
means that no matter what you set for the plot width, the plot will always
try to select data at the edge of the domain. If you wanted to avoid this,
you'd need to modify yt so that ds.all_data() is not assigned to `dd`, here:

https://bitbucket.org/yt_analysis/yt/src/yt/yt/visualization/plot_window.py?at=yt&fileviewer=file-view-default#plot_window.py-1528

The underlying issue is that yt is not very friendly when you try to select
data outside of the simulation domain. If your data has periodic boundary
conditions, everything works fine, but no other boundary conditions has
been implemented. Doing a proper job of generating ghost zones at domain
boundary requires some care, though, and no one has wanted to add this
feature.

-Nathan

On Wed, Jun 1, 2016 at 6:56 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> Hi all,
>
> I am trying my hand at off axis projections, and having some trouble
> setting the width of the projection.  Specifically, unless I make the width
> much too small to be useful to me, I get an error that my region is outside
> of the box boundaries.
>
>
> Here is the bit of code I have written:
>
>     L = [0.0,0.93969,-0.342]
>     c = [0.5,0.5,0.5]
>     N = 1028
>     north_vector = [0,-0.342,0.93969]
>     plot12 =
> yt.OffAxisProjectionPlot(ds,L,'density',width=(80,'kpc'),north_vector=north_vector)
>     plot12.save()
>
> My whole box is about 215 kpc wide, but unless I set my width to be 35 kpc
> I get this error (or something like it with the edge values listed at the
> end varying).  When I use 35 kpc it looks probably right, although it is
> just the center of a galaxy so a bit hard to say.
>
> Traceback (most recent call last):
>   File "yt_yslices_allout.py", line 57, in <module>
>     plot12 =
> yt.OffAxisProjectionPlot(ds,L,'density',width=(80,'kpc'),north_vector=north_vector)
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 1650, in __init__
>     periodic=False, oblique=True, fontsize=fontsize)
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 625, in __init__
>     PlotWindow.__init__(self, *args, **kwargs)
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 205, in __init__
>     self._setup_plots()
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 693, in _setup_plots
>     self._recreate_frb()
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 1656, in _recreate_frb
>     super(OffAxisProjectionPlot, self)._recreate_frb()
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line
> 265, in _recreate_frb
>     self._frb._get_data_source_fields()
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py",
> line 164, in _get_data_source_fields
>     self[f]
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py",
> line 577, in __getitem__
>     north_vector=dd.north_vector, method=dd.method)
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/off_axis_projection.py",
> line 194, in off_axis_projection
>     for i, (grid, mask) in enumerate(data_source.blocks):
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 1022, in blocks
>     for io_chunk in self.chunks([], "io"):
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 1076, in chunks
>     self.get_data() # Ensure we have built ourselves
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 1110, in get_data
>     self.index._identify_base_chunk(self)
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/geometry/grid_geometry_handler.py",
> line 283, in _identify_base_chunk
>     gi = dobj.selector.select_grids(self.grid_left_edge,
>   File
> "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 1071, in selector
>     self._selector = sclass(self)
>   File "yt/geometry/selection_routines.pyx", line 848, in
> yt.geometry.selection_routines.RegionSelector.__init__
> (yt/geometry/selection_routines.c:15619)
> RuntimeError: Error: yt attempted to read outside the boundaries of a
> non-periodic domain along dimension 1.
> Region left edge = -0.0320252970485 code_length, Region right edge =
> 1.03202529705 code_length
> Dataset left edge = 0.0 code_length, Dataset right edge = 1.0 code_length
>
> This commonly happens when trying to compute ghost cells up to the domain
> boundary. Two possible solutions are to load a smaller region that does not
> border the edge or override the periodicity for this dataset.
>
>
> Can anyone help me?  Thanks,
> Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> _______________________________________________
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>
>
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