[yt-users] Streamlines for FLASH in yt

[Michael Zingale]

I don't think that (0,0,0) as a corner is a problem, but as John suggested,
boundary conditions can be.  A lot of yt assumes triply periodic BCs (I
suspect because these are common in cosmology).  You might try manually
resetting the BCs in the yt data set object to periodic to see if that
helps.  I've done this as:

    ds.periodicity = (True, True, True)



On Thu, Jul 30, 2015 at 9:34 PM, John ZuHone <jzuhone at 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
> (m) 781-708-5004
> jzuhone at space.mit.edu
> jzuhone at gmail.com
> http://www.jzuhone.com
>
> On Jul 30, 2015, at 9:30 PM, Mikhail Klassen <klassm at 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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-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
github: http://github.com/zingale
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