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

[Matthew Turk]

Hi Jeff,

yt assumed periodicity, simply because that covered the vast majority
of the situations that the ghost zones were used in -- it only becomes
an issue in the grids that touch the domain edges.  You can see this
in yt/utilities/data_point_utilities.c around line 1014 where it takes
the modulo of the integer location with dw[].  This is something of
obtuse code, but I'd be happy to help modify it to meet your needs.

Rick -- I think it would be very valuable if you could assist Dave in
making this option available in the main Enzo branch.  At that point,
a simple subclass of the IOHandler would handle obtaining the ghost
zones; this would also speed up volume rendering substantially.

-Matt

On Sat, Oct 23, 2010 at 9:26 AM, Rick Wagner <rwagner at physics.ucsd.edu> wrote:
> 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
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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