[yt-dev] Issue #763: Covering grid does not get filled out for a tightly nested AMR dataset (yt_analysis/yt)

[Nathan Goldbaum]

New issue 763: Covering grid does not get filled out for a tightly nested AMR dataset
https://bitbucket.org/yt_analysis/yt/issue/763/covering-grid-does-not-get-filled-out-for

Nathan Goldbaum:

While I was helping Alex Bogert out with a visualization of my galaxy dataset, we noticed some odd behavior in the covering grid.  This is exposed in the HiResIsolatedGalaxy dataset on yt-project.org/data using the following script:

```
#!python

from yt.mods import *
pf = load('HiResIsolatedGalaxy/DD0044/DD0044')
cgrid = pf.h.covering_grid(5, np.array([0.53, 0.53, 0.53]), np.array([256]*3))
print cgrid['Density']
```

On the current 3.0 tip, this prints:

```
[[[  4.14182811e-25   1.75059046e-28   1.29468963e-28 ...,   1.29245039e-30
     1.29245039e-30   0.00000000e+00]
  [  1.13112951e-24   1.50869295e-28   1.00778753e-28 ...,   1.29245039e-30
     1.29245039e-30   0.00000000e+00]
  [  5.55295171e-25   1.26780190e-28   7.13453664e-29 ...,   1.29245039e-30
     1.29245039e-30   0.00000000e+00]
  ...,
```

(cut off for clarity)

The zero values should not be there since this is an AMR dataset with valid data over the region covered by the covering grid.

One possibly weird property of this dataset is that it's quite tightly nested, particularly near the maximum refinement level, as you can clearly see in this image: http://i.imgur.com/7kSwXJk.png

No idea if the nesting is important - would love some input from someone who is more familiar with the covering grid code.  

FWIW, this issue only appears to be reproducible for this one dataset, I see no similar issue for `IsolatedGalaxy`, another nested AMR sim.