[yt-users] Problem with covering grid

[Elizabeth Tasker]

Hi,

I've hit a problem with the latest version of yt and covering grid that is
linked with the number of ghostzones. My code looked like:

for dim in range(3):

      left.append(cloud_position[c][dim] - 0.5*width[dim])
      right.append(cloud_position[c][dim] + 0.5*width[dim])
      dims.append(int(round((right[dim]-left[dim])/cellsize)))

    cgrid = pf.h.covering_grid(level,
                               left_edge = left,
                               dims=dims,
                               num_ghost_zones=2)


but gives me:

TypeError                                 Traceback (most recent call last)
/home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
----> 1 execfile("export_hdf5_cube.py")

/home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
     51                                left_edge = left,
     52                                dims=dims,
---> 53                                num_ghost_zones=2)
     54
     55

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
__init__(self, level, left_edge, dims, fields, pf, num_ghost_zones,
use_pbar, **kwargs)
   3689         self.level = level
   3690         rdx = self.pf.domain_dimensions*self.pf.refine_by**level
-> 3691         rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1   #
issue 602
   3692         self.dds = self.pf.domain_width / rdx.astype("float64")
   3693         self.ActiveDimensions = np.array(dims, dtype='int32')

TypeError: unsupported operand type(s) for -: 'list' and 'int'




This happens regardless of whether I use num_ghost_zones or not. If I don't
have ghost_zones set, the error occurs at line 52, but still points to line
3691. Dims and left look fine:

In [9]: dims
Out[9]: [64, 64, 64]

In [10]: left
Out[10]: [20.424700000000001, 11.512700000000001, 15.7158]

In [11]: level
Out[11]: 5

In [14]: rdx = pf.domain_dimensions*pf.refine_by**level
In [15]: rdx
Out[15]: array([4096, 4096, 4096])


If I set num_ghost_zones = na.array([0,0,0]) then it runs. However, if I
then try

 cgrid["x"]

I hit more problems circulating around the same area:

ValueError                                Traceback (most recent call last)
/home/tasker/yt-new2/src/yt-hg/scripts/iyt in <module>()
----> 1 cgrid["y"]

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
__getitem__(self, key)
    316             if key not in self.fields:
    317                 self.fields.append(key)
--> 318             self.get_data(key)
    319         return self.field_data[key]
    320

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
get_data(self, fields)
   3733                 try:
   3734                     #print "Generating", field
-> 3735                     self._generate_field(field)
   3736                     continue
   3737                 except NeedsOriginalGrid, ngt_exception:

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/data_containers.pyc in
_generate_field(self, field)
   3764         if self.pf.field_info.has_key(field):
   3765             # First we check the validator; this might even raise!
-> 3766             self.pf.field_info[field].check_available(self)
   3767             self[field] = self.pf.field_info[field](self)
   3768         else: # Can't find the field, try as it might

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc in
check_available(self, data)
    354         """
    355         for validator in self.validators:
--> 356             validator(data)
    357         # If we don't get an exception, we're good to go
    358         return True

/home/tasker/yt-new2/src/yt-hg/yt/data_objects/field_info_container.pyc in
__call__(self, data)
    482         if not data._spatial:
    483             raise NeedsGridType(self.ghost_zones,self.fields)
--> 484         if self.ghost_zones <= data._num_ghost_zones:
    485             return True
    486         raise NeedsGridType(self.ghost_zones,self.fields)

ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()


cgrid["Density"] and the velocities are fine.

I'm suspecting this is because the position calculation in the code is not
expecting an array for the ghost zone number?

Oddly, I see from the mailing list is this reminiscent of a problem nyx was
having.

Elizabeth
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