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

[David Collins]

Rick is correct, I do have a version that outputs ghost zones. I can
stick that in on Monday, if you think that would help.  Does YT know
how to read datasets with ghost zones?  And will you need to be able
to restart from datasets with the ghosts written?  (not something I've
implemented, but not hard to do)

d.

On Sat, Oct 23, 2010 at 11:07 AM, j s oishi <jsoishi at gmail.com> wrote:
> Hi everyone,
>
> Thanks! I'm not sure it's really worth it to modify yt in this way
> until I can figure out how to get enzo to dump ghost zones, and I'm
> not sure that's necessary either if I can figure out my bug.
>
> I appreciate all your help.
>
> j
>
> On Sat, Oct 23, 2010 at 10:33 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>> 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
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>



-- 
Sent from my Stone Tablet and carried by my Pterodactyl.