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

[Rick Wagner]

Hi John,

Actually, some users have modified Enzo to output ghost zones (e.g., Dave), but it's certainly not the norm.

--Rick

On Oct 23, 2010, at 9:12 AM, John Wise <jwise at astro.princeton.edu> wrote:

> 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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