[yt-users] ghost zone validator issue.

Fri Sep 20 22:57:26 PDT 2013

Please ignore this thread.  I've found the problem.  It was not 
yt-related.

Thanks.

On Fri, 20 Sep 2013, Andrew Cunningham wrote:

> 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)
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