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@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.

Nathan

On Thursday, July 30, 2015, John ZuHone <jzuhone@gmail.com> wrote:
Hi Mikhail,

Sorry you're having trouble--any chance you can post your script using paste.yt-project.org 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?

Best,

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
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jzuhone@gmail.com
http://www.jzuhone.com

On Jul 30, 2015, at 9:30 PM, Mikhail Klassen <klassm@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 website.

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 code_length
Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19 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.

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?

Thanks,
Mikhail

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