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

[Cameron Hummels]

I gotcha.  And even though the dataset used in the 2.x docs was
non-periodic, yt assumed it was periodic and all the ghost-zones were
defined.  I see.

To address this, I like the idea of either including an extra layer of
ghost-zone cells around non-periodic datasets, so that fields like
vorticity, shear, etc. *are* defined for these datasets, but at the very
least, if we don't do this, could we have an error message describing that
such a field is not defined for non-periodic datasets?


On Thu, Jun 26, 2014 at 6:23 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> 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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> >
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>



-- 
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
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