Argh, sorry, Mike is right, it should be (True, True, True).
Does the error message not show the explicit code example? If not it
probably should, "override the periodicity" isn't clear enough unless you
know more about yt internals than we should expect.
On Thursday, July 30, 2015, Nathan Goldbaum <nathan12343(a)gmail.com> wrote:
You can do:
ds.periodicity = (1, 1, 1)
Technically this is wrong for your dataset, but if you don't care what
happens at the boundary it should be fine.
There's an open issue to do boundary conditions for yt's ghost
zones properly, but so far no one has taken it up.
On Thursday, July 30, 2015, John ZuHone <jzuhone(a)gmail.com
> Hi Mikhail,
> Sorry you're having trouble--any chance you can post your script using
or a similar paste service? It'll be easier to
> figure out what's going on then.
> By the way, what are your simulation's boundary conditions?
> John Z
> John ZuHone
> Kavli Center for Astrophysics and Space Research
> Massachusetts Institute of Technology
> 77 Massachusetts Ave., 37-582G
> Cambridge, MA 02139
> (w) 617-253-2354
> (m) 781-708-5004
> On Jul 30, 2015, at 9:30 PM, Mikhail Klassen <klassm(a)mcmaster.ca> wrote:
> I'm trying to plot 3D streamlines from a FLASH (v.4) dataset. I've based
> my streamlines script off the version presented on the yt-project.org
> I consistently get an error about going up the ghost cells in my volume.
> The error message is:
> RuntimeError: Error: yt attempted to read outside the boundaries of a
>> non-periodic domain along dimension 0.
>> Region left edge = -3e+18 code_length, Region right edge = 4.5e+18
>> Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19
>> 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.
> My FLASH datasets have x/y/zmin = 0.0 and x/y/zmax 1.2e19 cm.
> I seems like yt is trying to read outside my domain, or is bumping up
> against the guardcells and I have no idea how to prevent it from doing
> this. I have tried inspecting the code for an obvious solution. A very
> similar error shows up when I try to make 1D profiles of the entire dataset
> (dd = ds.all_data()).
> is it possible that yt doesn't support volumes where the (0,0,0)
> coordinate is a corner of the volume? Any easy solution to the above issue?
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