<div dir="ltr"><div>setting ds.periodicity worked like a charm! Thanks!<br><br></div>-Stephanie<br></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br><div class="gmail_quote">On Wed, Jun 1, 2016 at 7:11 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">The easiest way to workaround this issue is to do:<div><br></div><div>ds.periodicity = (True, True, True)</div><div><br></div><div>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:</div><div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/src/yt/yt/visualization/plot_window.py?at=yt&fileviewer=file-view-default#plot_window.py-1528" target="_blank">https://bitbucket.org/yt_analysis/yt/src/yt/yt/visualization/plot_window.py?at=yt&fileviewer=file-view-default#plot_window.py-1528</a></div><div><br></div><div>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.</div><div><br></div><div>-Nathan</div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Wed, Jun 1, 2016 at 6:56 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><div><div><div><div>Hi all,<br><br></div>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. <br><br><br></div><div>Here is the bit of code I have written:<br><br> L = [0.0,0.93969,-0.342]<br> c = [0.5,0.5,0.5] <br> N = 1028<br> north_vector = [0,-0.342,0.93969]<br> plot12 = yt.OffAxisProjectionPlot(ds,L,'density',width=(80,'kpc'),north_vector=north_vector)<br> plot12.save()<br><br></div>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.<br><br>Traceback (most recent call last):<br> File "yt_yslices_allout.py", line 57, in <module><br> plot12 = yt.OffAxisProjectionPlot(ds,L,'density',width=(80,'kpc'),north_vector=north_vector)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1650, in __init__<br> periodic=False, oblique=True, fontsize=fontsize)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 625, in __init__<br> PlotWindow.__init__(self, *args, **kwargs)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 205, in __init__<br> self._setup_plots()<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 693, in _setup_plots<br> self._recreate_frb()<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1656, in _recreate_frb<br> super(OffAxisProjectionPlot, self)._recreate_frb()<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 265, in _recreate_frb<br> self._frb._get_data_source_fields()<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py", line 164, in _get_data_source_fields<br> self[f]<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.py", line 577, in __getitem__<br> north_vector=dd.north_vector, method=dd.method)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/off_axis_projection.py", line 194, in off_axis_projection<br> for i, (grid, mask) in enumerate(data_source.blocks):<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1022, in blocks<br> for io_chunk in self.chunks([], "io"):<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1076, in chunks<br> self.get_data() # Ensure we have built ourselves<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1110, in get_data<br> self.index._identify_base_chunk(self)<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/geometry/grid_geometry_handler.py", line 283, in _identify_base_chunk<br> gi = dobj.selector.select_grids(self.grid_left_edge,<br> File "/home/stonnes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1071, in selector<br> self._selector = sclass(self)<br> File "yt/geometry/selection_routines.pyx", line 848, in yt.geometry.selection_routines.RegionSelector.__init__ (yt/geometry/selection_routines.c:15619)<br>RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 1.<br>Region left edge = -0.0320252970485 code_length, Region right edge = 1.03202529705 code_length<br>Dataset left edge = 0.0 code_length, Dataset right edge = 1.0 code_length<br><br>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.<br><br><br></div>Can anyone help me? Thanks,<br></div>Stephanie<br><br clear="all"><div><div><div><div><div><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
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