[yt-dev] Non-periodic datasets and ghost zones

[Matthew Turk]

On Thu, Jun 26, 2014 at 8:22 AM, Cameron Hummels <chummels at gmail.com> wrote:
> Is it clear why this issue cropped up in 3.0, but not in 2.x?  I don't
> remember the vorticity_squared field being a problem in this cookbook recipe
> in the 2.x docs.  What change broke this functionality?
>

I'll reply to Mike's email later, but the issue here is that we now no
longer assume periodicity.  So if you ask for a region that extends
off the edge of the domain, and your data is not periodict, it won't
wrap around.

> Cameron
>
>
> On Wed, Jun 25, 2014 at 3:49 PM, Michael Zingale
> <michael.zingale at stonybrook.edu> wrote:
>>
>> There are a lot of different types of boundary conditions, and some codes
>> take different actions depending on the variable, so it would be difficult
>> to support everything.  I have the Maestro front-end reading in the boundary
>> type, but I usually have to override it to periodic to get yt to work.
>>
>> One option is to provide just the minimum types of boundaries, a
>> zero-gradient/Neumann/outflow, and a reflection (perhaps that does
>> odd-reflection for vectors normal to the interface).  This should cover most
>> of the standard use cases (maybe a survey of what types of boundaries people
>> use would help?).  To close the remaining gap, there could be a standard
>> function interface that a user or frontend writer could provide to handle
>> "custom" BCs.
>>
>> It would also be useful to know what routines need boundary conditions and
>> how many ghost cells are needed.
>>
>>
>> On Wed, Jun 25, 2014 at 6:33 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>>
>>> Maybe just fill the ghost zones with zeros?  If we're feeling really
>>> ambitious we could read in the boundary conditions for the simulation and do
>>> whatever is appropriate for those BCs.
>>>
>>>
>>> On Wed, Jun 25, 2014 at 3:25 PM, Matthew Turk <matthewturk at gmail.com>
>>> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> What should we do (in general) about non-periodic datasets and getting
>>>> ghost zones for the domain edges?
>>>>
>>>> This is the reason that the cookbook recipe
>>>> simple_slice_with_multiple_fields.py fails -- it's trying to get
>>>> vorticity (needs GZs) for a non-periodic dataset.
>>>>
>>>> Fixing the cookbook only requires swapping out the dataset, but I
>>>> thought we should probably open this discussion up a bit too.
>>>>
>>>> -Matt
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>>>
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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
>>
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>
>
>
> --
> Cameron Hummels
> Postdoctoral Researcher
> Steward Observatory
> University of Arizona
> http://chummels.org
>
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