[yt-users] error on plotting particle_density
Matthew Turk
matthewturk at gmail.com
Thu Jul 11 20:52:35 PDT 2013
Hi Mohammad,
There are a couple possible explanations. One is that there isn't
that much resolution in your simulation. Particle density is
calculated by depositing the particles themselves into the existing
grid cells; if the grid cells are coarse and the particles are
clustered, it could look like that. I've run this exact script on the
Enzo_64/DD0043
What is perhaps more worrisome is that your density is very, very low
-- since this is an unweighted projection, it should be in column
density. It almost looks to me like there is a problem with the
conversion factor or something with your data, or potentially with the
mass. Can you try plotting a slice of this, or an unweighted
projection of the full domain?
-Matt
PS There were issues with the mailing lists yt-users and yt-dev this
evening; our ISP has resolved them so if anyone reading this had
issues posting earlier they should now be fixed.
On Thu, Jul 11, 2013 at 9:17 PM, mohammad safarzadeh
<mtsafarzadeh at gmail.com> wrote:
> I installed YT all over again,
> now the plots that I get are a bit weird. it sounds like it is putting cubes
> around haloes:
> from this command:
> p = ProjectionPlot(pf, "x", "particle_density",[ 0.5808,0.5398, 0.4504
> ],(4.0,'mpc'))
> the image is here:
> http://i.imgur.com/z4QA2uz.png
>
> -Mohammad
>
>
> On Wed, Jul 10, 2013 at 3:58 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> Hi Mohammad,
>>
>> Sorry you're having trouble. In my version of cde0a641f1bf , the line
>> numebrs don't match up with yours. In particular, my _pdensity
>> function starts on line 1010, and looks like this:
>>
>> def _pdensity(field, data):
>> blank = np.zeros(data.ActiveDimensions, dtype='float64')
>> if data["particle_position_x"].size == 0: return blank
>> CICDeposit_3(data["particle_position_x"].astype(np.float64),
>> data["particle_position_y"].astype(np.float64),
>> data["particle_position_z"].astype(np.float64),
>> data["ParticleMass"],
>> data["particle_position_x"].size,
>> blank, np.array(data.LeftEdge).astype(np.float64),
>> np.array(data.ActiveDimensions).astype(np.int32),
>> np.float64(data['dx']))
>> np.divide(blank, data["CellVolume"], blank)
>> return blank
>> add_field("particle_density", function=_pdensity,
>> validators=[ValidateGridType()],
>> display_name=r"\mathrm{Particle}\/\mathrm{Density}")
>>
>> The only buffer there that's not cast to float64 is
>> data["ParticleMass"]. I don't know why your line numbers and mine do
>> not match up, since you don't have a + in your source file, however if
>> your function matches mine please try adding the appropriate
>> .astype(np.float64). In 3.0 we have abstracted some of this out to
>> use a deposit function that handles types better.
>>
>> -Matt
>>
>> On Wed, Jul 10, 2013 at 3:38 PM, mohammad safarzadeh
>> <mtsafarzadeh at gmail.com> wrote:
>> > Hi,
>> > I get this error when trying to do a projection plot:
>> > ----> 9 p = ProjectionPlot(pf, "x", "particle_density",[ 0.5808,0.5398,
>> > 0.4504 ],(4.0,'mpc'))
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> > __init__(self, pf, axis, fields, center, width, axes_unit, weight_field,
>> > max_level, origin, fontsize, field_parameters, data_source)
>> > 1347 if field_parameters is None: field_parameters = {}
>> > 1348 proj = pf.h.proj(axis, fields,
>> > weight_field=weight_field,
>> > max_level=max_level,
>> > -> 1349 center=center, source=data_source,
>> > **field_parameters)
>> > 1350 PWViewerMPL.__init__(self, proj, bounds, origin=origin,
>> > fontsize=fontsize)
>> > 1351 self.set_axes_unit(axes_unit)
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > __init__(self, axis, field, weight_field, max_level, center, pf, source,
>> > node_name, field_cuts, preload_style, serialize, style, **kwargs)
>> > 1758 self.preload_style = preload_style
>> > 1759 self._deserialize(node_name)
>> > -> 1760 self._refresh_data()
>> > 1761 if self._okay_to_serialize and self.serialize:
>> > self._serialize(node_name=self._node_name)
>> > 1762
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > _refresh_data(self)
>> > 318 """
>> > 319 self.clear_data()
>> > --> 320 self.get_data()
>> > 321
>> > 322 def keys(self):
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > get_data(self, fields)
>> > 1859 if g.Level == level],
>> > 1860 self.get_dependencies(fields),
>> > self.hierarchy.io)
>> > -> 1861 self._add_level_to_tree(tree, level, fields)
>> > 1862 mylog.debug("End of projecting level level %s,
>> > memory
>> > usage %0.3e",
>> > 1863 level, get_memory_usage()/1024.)
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > _add_level_to_tree(self, tree, level, fields)
>> > 1981 % (level, self._max_level),
>> > len(grids_to_project))
>> > 1982 for pi, grid in enumerate(grids_to_project):
>> > -> 1983 self._add_grid_to_tree(tree, grid, fields,
>> > zero_out,
>> > dls)
>> > 1984 pbar.update(pi)
>> > 1985 grid.clear_data()
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > _add_grid_to_tree(self, tree, grid, fields, zero_out, dls)
>> > 1925 if zero_out: weight_data[grid.child_indices] = 0
>> > 1926 masked_data = [fd.astype('float64') * weight_data
>> > -> 1927 for fd in
>> > self._get_data_from_grid(grid,
>> > fields)]
>> > 1928 wdl = 1.0
>> > 1929 else:
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > save_state(self, grid, field, *args, **kwargs)
>> > 93 old_keys = grid.field_data.keys()
>> > 94 grid.field_parameters = self.field_parameters
>> > ---> 95 tr = func(self, grid, field, *args, **kwargs)
>> > 96 grid.field_parameters = old_params
>> > 97 grid.field_data = YTFieldData( [(k, grid.field_data[k])
>> > for
>> > k in old_keys] )
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> > in
>> > _get_data_from_grid(self, grid, fields)
>> > 2003 else:
>> > 2004 bad_points = 1.0
>> > -> 2005 return [grid[field] * bad_points for field in fields]
>> > 2006
>> > 2007 def _gen_node_name(self):
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
>> > __getitem__(self, key)
>> > 155 """
>> > 156 if key not in self.field_data:
>> > --> 157 self.get_data(key)
>> > 158 return self.field_data[key]
>> > 159
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
>> > get_data(self, field, convert)
>> > 198 else: raise
>> > 199 else:
>> > --> 200 self._generate_field(field)
>> > 201 return self.field_data[field]
>> > 202
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in
>> > _generate_field(self, field)
>> > 143 self[field] = temp_array[sl]
>> > 144 else:
>> > --> 145 self[field] = self.pf.field_info[field](self)
>> > 146 else: # Can't find the field, try as it might
>> > 147 raise exceptions.KeyError(field)
>> >
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.pyc
>> > in __call__(self, data)
>> > 393 ii = self.check_available(data)
>> > 394 original_fields = data.keys() # Copy
>> > --> 395 dd = self._function(self, data)
>> > 396 dd *= self._convert_function(data)
>> > 397 for field_name in data.keys():
>> >
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/data_objects/universal_fields.pyc in
>> > _pdensity(field, data)
>> > 982 blank,
>> > np.array(data.LeftEdge).astype(np.float64),
>> > 983
>> > np.array(data.ActiveDimensions).astype(np.int32),
>> > --> 984 np.float64(data['dx']))
>> > 985 return blank
>> > 986 add_field("particle_density", function=_pdensity,
>> >
>> > /home/safarzadeh/yt-x86_64/src/yt-hg/yt/utilities/lib/CICDeposit.so in
>> > yt.utilities.lib.CICDeposit.CICDeposit_3
>> > (yt/utilities/lib/CICDeposit.c:1485)()
>> >
>> > ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float'
>> >
>> > are there alternative ways around it?
>> >
>> > (yt-x86_64)[safarzadeh at hecate yt-x86_64]$ yt instinfo
>> >
>> > yt module located at:
>> > /home/safarzadeh/yt-x86_64/src/yt-hg
>> > The supplemental repositories are located at:
>> > /home/safarzadeh/yt-x86_64/src/yt-supplemental
>> >
>> > The current version of the code is:
>> >
>> > ---
>> > cde0a641f1bf
>> > ---
>> >
>> > This installation CAN be automatically updated.
>> > Could not determine when yt stack was last updated.
>> >
>> >
>> >
>> > Regards,
>> > Mohammad
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
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