[yt-users] Problem with covering grid
Matthew Turk
matthewturk at gmail.com
Fri Apr 25 01:44:09 PDT 2014
Hi Elizabeth,
On Fri, Apr 25, 2014 at 4:38 AM, Elizabeth Tasker
<tasker at astro1.sci.hokudai.ac.jp> wrote:
> 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
I've just checked, and I am able to replicate the error with this
changeset using this script:
from yt.mods import *
pf = load("IsolatedGalaxy/galaxy0030/galaxy0030")
level = 0
left = [0.0, 0.0, 0.0]
dims = [16, 16, 16]
cgrid = pf.h.covering_grid(level, left_edge = left, dims=dims,
num_ghost_zones=2)
However, when I update to the current tip of the yt branch,
1a67d558b51c, it works. :)
-Matt
>
>
> 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
>> >
>> > _______________________________________________
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>> >
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