[Yt-dev] Radius Calculation

[Britton Smith]

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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