[yt-users] RuntimeError with surface

Slavin, Jonathan jslavin at cfa.harvard.edu
Wed Mar 2 09:15:44 PST 2016


Hi all,

I have some 3D data that I'd like to visualize using iso-surfaces.  The
data are for an explosion at the center and in cartesian coordinates with
reflecting boundary conditions on the left edges such that it is expanding
in one octant of a 3D space.  I have tried a few different approaches and I
keep running into the RuntimeError:
"Error: yt attempted to read outside the boundaries of a non-periodic
domain along dimension 0.
...
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."

So this is after I loaded a smaller region.  I don't want to exclude the
planes along x = 0, y= 0 and z = 0 because then I'll be excluding the
explosion center.  It's not clear to me how to "exclude the periodicity for
the dataset".  Any help would be appreciated.

​Thanks,
Jon​

-- 
________________________________________________________
Jonathan D. Slavin                 Harvard-Smithsonian CfA
jslavin at cfa.harvard.edu       60 Garden Street, MS 83
phone: (617) 496-7981       Cambridge, MA 02138-1516
cell: (781) 363-0035             USA
________________________________________________________
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