[yt-users] Problem with covering grid

Fri Apr 25 01:38:07 PDT 2014

Hi Matt,

Thanks! This is:

yt module located at:
    /home/tasker/yt-new2/src/yt-hg

The current version of the code is:

---
81c2f6f5f983
---

Elizabeth

On 25 April 2014 17:34, Matthew Turk <matthewturk at gmail.com> wrote:

> 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
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140425/56c4a6bd/attachment.htm>