[yt-users] Problem with covering grid

[Matthew Turk]

Hi Elizabeth,

On Fri, Apr 25, 2014 at 3:40 AM, Elizabeth Tasker
<tasker at astro1.sci.hokudai.ac.jp> wrote:
> 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.

Yes, and it feels like this exact issue -- where dims are lists, not
arrays -- gets fixed over and over and over again.  :(  Can you report
which changeset you're on, and I'll push a fix?

-Matt

>
> Elizabeth
>
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