[Yt-dev] Radius Calculation

[Matthew Turk]

Okay, so suddenly it occurs to me -- if your domain width is 1.0, then
this is in fact just a subset of your domain, and it could be correct.
 I forgot about parallel root grid IO.  What happens if you plot a
slice through the center of the domain of the new field?

pc = PlotCollection(pf, center=[0.5,0.5,0.5])
pc.add_slice("NewRadius", 0)
pc.add_slice("Radius", 0)
pc.save("new")

That should show us if it's actually giving the right results or not.
Apologies; I completely forgot about decomposed root grids when I
wrote that script.

On Fri, Apr 17, 2009 at 9:01 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hm, this looks wrong to me.  Clearly something I have not considered
> -- over here myi mages look like the attached.  What's the value for
> the domain width?  This is confusing to me, as I really thought it
> would work!
>
> Can you try with a projection?  It should work, right through the
> domain, and it should tell us what we're looking for.  Or, jsut
> straight-up slices of NewRadius.  I'll try some stuff too.
>
> On Fri, Apr 17, 2009 at 8:48 PM, Britton Smith <brittonsmith at gmail.com> wrote:
>> I just tried your script with some data I have here.  I've attached the
>> images.  I can't really tell if this is right or not.  I think another way
>> to test this would be to do a projection with a periodic sphere as the
>> source object.  If you throw a sphere that overlaps the domain boundary to a
>> projection, it should be quite clear if it's doing what it's supposed to.
>> Does that sound right?
>>
>> Britton
>>
>> On Fri, Apr 17, 2009 at 8:17 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>>
>>> Oops, just as a note, there's an error in the paste -- the second plot
>>> of "NewRadius" should be of "Radius".
>>>
>>> Thanks guys...
>>>
>>> -Matt
>>>
>>> On Fri, Apr 17, 2009 at 7:16 PM, Matthew Turk <matthewturk at gmail.com>
>>> wrote:
>>> > Hi guys,
>>> >
>>> > Can somebody review this?  I chatted with Jeff, and I believe it is
>>> > correct for periodic boxes, but I need somebody to look at it before I
>>> > commit it, as it is a rather crucial aspect of yt.  This changes the
>>> > way radius is calculated and should now work with periodic boundary
>>> > conditions.
>>> >
>>> > Here's the new field definition:
>>> >
>>> > def _NewRadius(field, data):
>>> >    center = data.get_field_parameter("center")
>>> >    DW = data.pf["DomainRightEdge"] - data.pf["DomainLeftEdge"]
>>> >    radius = na.zeros(data["x"].shape, dtype='float64')
>>> >    for i, ax in enumerate('xyz'):
>>> >        r = na.abs(data[ax] - center[i])
>>> >        radius += na.minimum(r, na.abs(DW[i]-r))**2.0
>>> >    na.sqrt(radius, radius)
>>> >    return radius
>>> >
>>> > the final argument in na.sqrt is the 'out' argument, to avoid temporary
>>> > arrays.
>>> >
>>> > I've committed a sample script here:
>>> >
>>> > http://paste.enzotools.org/show/101/
>>> >
>>> > which loads up a data dump, calculates the radius from [0.1, 0.1, 0.1]
>>> > at all points in the root grid, then plots the output.  It gives
>>> > correct min & max values for the radius.
>>> >
>>> > If I can get somebody else to sign off on this, I will commit the
>>> > necessary changes to _Radius and _ParticleRadius, as well as grid &
>>> > point selection for spheres.  We'll then have a fully-periodic
>>> > profiler, which will close #165.
>>> >
>>> > -Matt
>>> >
>>> > On Thu, Apr 16, 2009 at 11:39 AM, Matthew Turk <matthewturk at gmail.com>
>>> > wrote:
>>> >> Hi guys,
>>> >>
>>> >> I've been exploring the idea of changing radius to be correct for
>>> >> periodic boxes.  Right now it is incorrect; each component (x,y,z)
>>> >> should not have a distance greater than 0.5 * domain_size.  The
>>> >> easiest way to do this would be:
>>> >>
>>> >> rx = min( abs( x - center_x ), abs( x - center_x - domain_x) )
>>> >>
>>> >> I think the best way to do this is to set up a NumPy ufunc
>>> >>
>>> >>
>>> >> http://docs.scipy.org/doc/numpy/user/c-info.beyond-basics.html#creating-a-new-universal-function
>>> >>
>>> >> that accepts three arrays, along with the center and the domain width,
>>> >> and then returns the radius.  What do you all think?  Alternatively,
>>> >> I'm thinking maybe just a regular function that gets the arrays and
>>> >> returns one would be better; the ufunc machinery is a bit complicated
>>> >> and I might get confused.  Once I come up with it, will somebody be
>>> >> able to look over my work?
>>> >>
>>> >> -Matt
>>> >>
>>> >
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