[yt-users] ghost zones and non-periodic boundary conditions

[John Wise]

Hi Jeff,

I'm not exactly sure what kind of assumptions the retrieve_ghost_zones() 
routine makes about the boundary conditions, but I can answer your Enzo 
question.  Enzo never outputs the ghost zones, and they are always 
recreated when restarting a simulation.  By your description, it looks 
like yt is assuming periodic boundary conditions and filling the ghost 
zones.  I tried to look in the source, but I couldn't find where 
periodicity is used in the covering_grid, and whether that can be 
changed to something else.

John

On 10/23/2010 02:50 AM, j s oishi wrote:
> Hi all,
>
> I have a question which is kind of a yt question and kind of an enzo
> question, so first off, my apologies to the non-enzo users. I have
> something that quite clearly appears to be a boundary value problem on
> a non-periodic boundary condition. My first method of attack is to
> load the (single) root grid data object with its ghost zones:
>
> pf = load(data)
> gz = pf.h.grids[0].retrieve_ghost_zones(2,'y-velocity')
>
> However, when I do this on a sample I believe not to have the bug, it
> appears that yt is loading periodic boundary conditions in the
> non-periodic direction: the first ghost zone on the lower y boundary
> is exactly equal to the second-to-top active zone, and the second
> lower y ghost zone exactly equals the top active zone. More
> concretely,
>
> gz['y-velocity'][:,0,2] always equals gz['y-velocity'][:,-4,2]
>
> and
>
> gz['y-velocity'][:,1,2] always equals gz['y-velocity'][:,-3,2]
>
> This is very clear in the (2D) case at hand, since the velocity field
> is a large gradient in the y-direction.
>
> Is it possible that enzo is not outputting its ghost zones, and yt is
> simply filling using a periodic method? Or does enzo always output
> ghost zones, and this is simply a manifestation of my bug?
>
> I realize this is not a very clear question, but I'm a bit confused myself.
>
> thanks,
>
> j
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