BUG: artificacts in vorticity for athena

[chrishavlin]

Plots of vorticity (and presumably any variable that needs a derivative) have artifacts aligned with grid boundaries where the resolution changes:

import yt 
ds = yt.load_sample("AM06")
slc = yt.SlicePlot(ds, 'x', ('gas', 'vorticity_x'), window_size=(4,4))
slc.save('vort_x.png')
slc.annotate_grids()
slc.save('vort_x_with_grids.png')

Also note that you do get a RuntimeWarning:

/home/chavlin/src/yt_general/yt/yt/data_objects/construction_data_containers.py:1531: RuntimeWarning: 
Something went wrong during field computation. This is likely due to missing ghost-zones support in 
class <class 'weakref.ProxyType'>

So presumably this is a known issue, but I didn't see a clear corresponding open issue so I thought it was worth opening a new report to document it. There are, however, a number of open and closed issues that are related to ghost zones and vorticity (in athena and other frontends):

• Handling athena file with ghost zones #2033
• fix: log error instead of crashing in smoothed grid computation if ghost-zones can't be reconstructed #2715
• Issue plotting vorticity from amrvac data #2710
• BUG: [AMRVAC] datafiles with ghost cells are not read correctly #3382
• The AMReX frontend crashes when attempting to read plotfiles with ghost cells #1419

[chrishavlin]

also, feel free to close this as a duplicate if I missed an open issue or if one of the linked ones handles this sufficiently :)

[matthewturk]

That is a super weird error I do not recognize. I believe that what we should look at is whether or not the "smoothed" covering grids are being used.

[chrishavlin]

I believe that what we should look at is whether or not the "smoothed" covering grids are being used.

That would be a yes, this call to retrieve_ghost_zones hardcodes a smoothed=True parameter, which results in using a smoothed covering grid to fill the ghost zones

yt/yt/geometry/grid_geometry_handler.py

Lines 380 to 384 in 9e483ce

	for og in giter:
	if ngz > 0:
	g = og.retrieve_ghost_zones(ngz, [], smoothed=True)
	else:
	g = og

[chrishavlin]

setting it to False to see what happens... it does run, and the magnitude of the artifacts is lower, but they're still there: