[yt-users] ghost zone validator issue.

[Andrew Cunningham]

I'm trying to compute d/dx(gravitational-potential) following the 
divergence of velocity cookbook recepie in the trunk version of yt-2.5. 
However, when I do this the data reader tries to read past the end of the 
dataset in the chombo file.  Do others see similar behavior with output 
from other codes or do I have a chombo-specific issue here?


# computes unlimited centered difference
def unlimited(right,center,left):
     return 0.5*(right-left)

def _Gx(field, data):
     sl_left = slice(None,-2,None)
     sl_right = slice(2,None,None)
     ds = data['dx'].flat[0]
     out = np.zeros(data['gravitational-potential'].shape, dtype='float64')
     out[1:-1,1:-1,1:-1] = 
-unlimited(data['gravitational-potential'][sl_right,1:-1,1:-1],data['gravitational-potential'][1:-1,1:-1,1:-1],data['gravitational-potential'][sl_left 
,1:-1,1:-1])/ds
     return out
add_field('Gx', function=_Gx, 
validators=[ValidateSpatial(ghost_zones=1,fields=['gravitational-potential'])], 
take_log=False)


Traceback (most recent call last):
   File "GradPhy.py", line 48, in <module>
     off = OffAxisSlicePlot(pf, [0,0,1], "Gx", center=center, width=(1000, 
"au"))
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 1454, in 
__init__
     oblique=True, fontsize=fontsize)
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 784, in 
__init__
     PWViewer.__init__(self, *args, **kwargs)
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 591, in 
__init__
     PlotWindow.__init__(self, *args,**kwargs)
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 307, in 
__init__
     self.set_window(bounds) # this automatically updates the data and plot
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 76, in 
newfunc
     args[0]._recreate_frb()
   File "/home/acunning/yt/yt/visualization/plot_window.py", line 359, in 
_recreate_frb
     self._frb._get_data_source_fields()
   File "/home/acunning/yt/yt/visualization/fixed_resolution.py", line 138, 
in _get_data_source_fields
     self[f]
   File "/home/acunning/yt/yt/visualization/fixed_resolution.py", line 424, 
in __getitem__
     self.data_source[item],
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 318, 
in __getitem__
     self.get_data(key)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 845, 
in get_data
     if self._generate_field(field):
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 345, 
in _generate_field
     self._generate_field_in_grids(field, ngt_exception.ghost_zones)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 355, 
in _generate_field_in_grids
     grid[field] = self.__touch_grid_field(grid, field)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 81, in 
save_state
     tr = func(self, grid, field, *args, **kwargs)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 359, 
in __touch_grid_field
     return grid[field]
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 147, in 
__getitem__
     self.get_data(key)
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 190, in 
get_data
     self._generate_field(field)
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 130, in 
_generate_field
     gz_grid = self.retrieve_ghost_zones(n_gz, f_gz, smoothed=True)
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 467, in 
retrieve_ghost_zones
     level, new_left_edge, **kwargs)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3856, 
in __init__
     AMRCoveringGridBase.__init__(self, *args, **kwargs)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3700, 
in __init__
     self._refresh_data()
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3717, 
in _refresh_data
     AMR3DData._refresh_data(self)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 306, 
in _refresh_data
     self.get_data()
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3909, 
in get_data
     self._get_data_from_grid(grid, fields_to_get)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 96, in 
save_state
     tr = func(self, grid, field, *args, **kwargs)
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3970, 
in _get_data_from_grid
     else gf for gf in (grid[field] for field in fields)]
   File "/home/acunning/yt/yt/data_objects/data_containers.py", line 3970, 
in <genexpr>
     else gf for gf in (grid[field] for field in fields)]
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 147, in 
__getitem__
     self.get_data(key)
   File "/home/acunning/yt/yt/data_objects/grid_patch.py", line 180, in 
get_data
     temp = self.hierarchy.io.pop(self, field)
   File "/home/acunning/yt/yt/utilities/io_handler.py", line 53, in pop
     return self._read_data_set(grid, field)
   File "/home/acunning/yt/yt/utilities/io_handler.py", line 82, in 
_read_data_set
     return self._read_data(grid, field)
   File "/home/acunning/yt/yt/frontends/chombo/io.py", line 62, in 
_read_data
     data = lev[self._data_string][start:stop]
   File 
"/usr/lib64/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg/h5py/highlevel.py", 
line 1207, in __getitem__
     selection = sel.select(self.shape, args, dsid=self.id)
   File 
"/usr/lib64/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg/h5py/selections.py", 
line 94, in select
     sel[args]
   File 
"/usr/lib64/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg/h5py/selections.py", 
line 261, in __getitem__
     start, count, step, scalar = _handle_simple(self.shape,args)
   File 
"/usr/lib64/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg/h5py/selections.py", 
line 512, in _handle_simple
     x,y,z = _translate_slice(arg, length)
   File 
"/usr/lib64/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg/h5py/selections.py", 
line 562, in _translate_slice
     raise ValueError("Start index %s out of range (0-%d)" % (start, 
length-1))
ValueError: Start index 10665984 out of range (0-10665983)