[yt-users] RuntimeError with surface

[Nathan Goldbaum]

Hi Jonathan,

That error message should probably include the workaround. Do the following:

ds.periodicity = (True, True, True)

-Nathan

On Wed, Mar 2, 2016 at 11:15 AM, Slavin, Jonathan <jslavin at cfa.harvard.edu>
wrote:

> 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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