[yt-users] Particles in FLASH output
Nathan Goldbaum
nathan12343 at gmail.com
Tue Apr 28 12:37:45 PDT 2015
On Tue, Apr 28, 2015 at 12:27 PM, Jason Galyardt <jason.galyardt at gmail.com>
wrote:
> Hi all,
>
> I've updated to the latest development release of yt (v3.2dev). I no
> longer get the ValueError to do with zero length selections when I do
> annotate_particles(). However, I don't get any particles in the plot
> either. Any other ideas?
>
Can you try:
p.annotate_particles((4, 'kpc'))
?
If that works, can you file a bug about annotate_particles not handling
widths that are YTQuantity instances correctly?
https://bitbucket.org/yt_analysis/yt/issues/new
>
> Thanks,
> Jason
>
> On Tue, Apr 28, 2015 at 2:56 PM, Yuan Li <bear0980 at gmail.com> wrote:
>
>> Hi Jason,
>>
>> I had trouble with Flash particles last year, and John ZuHone fixed the
>> bug. Could you try the newest yt3 and see if the problem goes away?
>>
>> Yuan
>>
>> On Tue, Apr 28, 2015 at 2:53 PM, Jason Galyardt <jason.galyardt at gmail.com
>> > wrote:
>>
>>> Nathan,
>>>
>>> I'm using yt version 3.0.2 (which I see is not quite current) on Debian
>>> 7 (wheezy). I tried to pastebin the iPython error traceback, but it failed
>>> with a complaint that the MySQL server has 'gone away'. With apologies to
>>> the list, here's the traceback:
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> ValueError Traceback (most recent call
>>> last)
>>> <ipython-input-49-3f118016da60> in <module>()
>>> ----> 1 p.annotate_particles((4.0,'kpc'))
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/visualization/plot_container.pyc
>>> in newfunc(*args, **kwargs)
>>> 68 rv = f(*args, **kwargs)
>>> 69 args[0]._plot_valid = False
>>> ---> 70 args[0]._setup_plots()
>>> 71 return rv
>>> 72 return newfunc
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/visualization/plot_window.pyc
>>> in _setup_plots(self)
>>> 860 label.set_fontproperties(fp)
>>> 861
>>> --> 862 self.run_callbacks(f)
>>> 863
>>> 864 if draw_axes is False:
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/visualization/plot_container.pyc
>>> in run_callbacks(self, f)
>>> 313 CallbackMaker = callback_registry[name]
>>> 314 callback = CallbackMaker(*args[1:], **kwargs)
>>> --> 315 callback(cbw)
>>> 316 for key in self.frb.keys():
>>> 317 if key not in keys:
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/visualization/plot_modifications.pyc
>>> in __call__(self, plot)
>>> 1053 pt = self.ptype
>>> 1054 gg = ( ( reg[pt, field_x] >= x0 ) & ( reg[pt, field_x]
>>> <= x1 )
>>> -> 1055 & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y]
>>> <= y1 ) )
>>> 1056 if self.minimum_mass is not None:
>>> 1057 gg &= (reg[pt, "particle_mass"] >= self.minimum_mass)
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/data_objects/data_containers.pyc
>>> in __getitem__(self, key)
>>> 238 return self.field_data[f]
>>> 239 else:
>>> --> 240 self.get_data(f)
>>> 241 # fi.units is the unit expression string. We depend on
>>> the registry
>>> 242 # hanging off the dataset to define this unit object.
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/data_objects/data_containers.pyc
>>> in get_data(self, fields)
>>> 665
>>> 666 read_particles, gen_particles =
>>> self.index._read_particle_fields(
>>> --> 667 particles, self,
>>> self._current_chunk)
>>> 668 for f, v in read_particles.items():
>>> 669 self.field_data[f] = self.ds.arr(v, input_units =
>>> finfos[f].units)
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/geometry/geometry_handler.pyc
>>> in _read_particle_fields(self, fields, dobj, chunk)
>>> 232 self._chunk_io(dobj, cache = False),
>>> 233 selector,
>>> --> 234 fields_to_read)
>>> 235 return fields_to_return, fields_to_generate
>>> 236
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/utilities/io_handler.pyc in
>>> _read_particle_selection(self, chunks, selector, fields)
>>> 148 # Here, ptype_map means which particles contribute to a
>>> given type.
>>> 149 # And ptf is the actual fields from disk to read.
>>> --> 150 psize = self._count_particles_chunks(chunks, ptf,
>>> selector)
>>> 151 # Now we allocate
>>> 152 # ptf, remember, is our mapping of what we want to read
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/utilities/io_handler.pyc in
>>> _count_particles_chunks(self, chunks, ptf, selector)
>>> 119 def _count_particles_chunks(self, chunks, ptf, selector):
>>> 120 psize = defaultdict(lambda: 0) # COUNT PTYPES ON DISK
>>> --> 121 for ptype, (x, y, z) in
>>> self._read_particle_coords(chunks, ptf):
>>> 122 psize[ptype] += selector.count_points(x, y, z, 0.0)
>>> 123 return dict(psize.items())
>>>
>>> /usr/local/lib/python2.7/dist-packages/yt/frontends/flash/io.pyc in
>>> _read_particle_coords(self, chunks, ptf)
>>> 72 start = p_ind[g1.id - g1._id_offset]
>>> 73 end = p_ind[g2.id - g2._id_offset + 1]
>>> ---> 74 x = np.asarray(p_fields[start:end, px],
>>> dtype="=f8")
>>> 75 y = np.asarray(p_fields[start:end, py],
>>> dtype="=f8")
>>> 76 z = np.asarray(p_fields[start:end, pz],
>>> dtype="=f8")
>>>
>>> /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.pyc in
>>> __getitem__(self, args)
>>> 312
>>> 313 # Perform the dataspace selection.
>>> --> 314 selection = sel.select(self.shape, args, dsid=self.id)
>>> 315
>>> 316 if selection.nselect == 0:
>>>
>>> /usr/lib/python2.7/dist-packages/h5py/_hl/selections.pyc in
>>> select(shape, args, dsid)
>>> 92
>>> 93 sel = SimpleSelection(shape)
>>> ---> 94 sel[args]
>>> 95 return sel
>>> 96
>>>
>>> /usr/lib/python2.7/dist-packages/h5py/_hl/selections.pyc in
>>> __getitem__(self, args)
>>> 259 return self
>>> 260
>>> --> 261 start, count, step, scalar =
>>> _handle_simple(self.shape,args)
>>> 262
>>> 263 self._id.select_hyperslab(start, count, step)
>>>
>>> /usr/lib/python2.7/dist-packages/h5py/_hl/selections.pyc in
>>> _handle_simple(shape, args)
>>> 510 for arg, length in zip(args, shape):
>>> 511 if isinstance(arg, slice):
>>> --> 512 x,y,z = _translate_slice(arg, length)
>>> 513 s = False
>>> 514 else:
>>>
>>> /usr/lib/python2.7/dist-packages/h5py/_hl/selections.pyc in
>>> _translate_slice(exp, length)
>>> 551 raise ValueError("Step must be >= 1 (got %d)" % step)
>>> 552 if stop == start:
>>> --> 553 raise ValueError("Zero-length selections are not
>>> allowed")
>>> 554 if stop < start:
>>> 555 raise ValueError("Reverse-order selections are not
>>> allowed")
>>>
>>> ValueError: Zero-length selections are not allowed
>>> ------------------------------------------------------------------------
>>>
>>> Let me know if any other info would be useful.
>>>
>>> Cheers,
>>> Jason
>>>
>>> On Tue, Apr 28, 2015 at 2:39 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Apr 28, 2015 at 11:37 AM, Nathan Goldbaum <
>>>> nathan12343 at gmail.com> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Tue, Apr 28, 2015 at 11:36 AM, Jason Galyardt <
>>>>> jason.galyardt at gmail.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I'm sure I've just overlooked some bit of documentation, but I'm
>>>>>> having trouble plotting particles generated by FLASH on top of the gas
>>>>>> density. I've been able to load a plot file with the associated particle
>>>>>> file via
>>>>>>
>>>>>> ds = yt.load(plotfileName, particle_filename=partfileName)
>>>>>>
>>>>>>
>>>>>> However, when I try to create a projection and annotate the particles
>>>>>> with
>>>>>>
>>>>>> p = yt.ProjectionPlot(ds, "y", "density")
>>>>>> p.annotate_particles(1.0) # ValueError!
>>>>>> # p.annotate_particles((4.0, 'kpc')) # ValueError!
>>>>>>
>>>>>>
>>>>> Can you pastebin the full error traceback? Which yt version are you
>>>>> using?
>>>>>
>>>>
>>>> Forgot to mention that you can get precise version information by
>>>> executing "yt version" at the bash command line.
>>>>
>>>>
>>>>>
>>>>>
>>>>>> I get a ValueError from h5py indicating that zero-length selections
>>>>>> are not allowed. I have also tried passing the full width of the simulation
>>>>>> domain to the annotation function without success. I suspect that this is a
>>>>>> user error stemming from differences between the way that Enzo and FLASH
>>>>>> store particle data. However, I can't find much in the way of documentation
>>>>>> or examples for the FLASH particle data format.
>>>>>>
>>>>>> Of course, it would also be handy to be able to write my own analysis
>>>>>> scripts using both gas and particles, but for now, I'll settle for any help
>>>>>> I can get on simple plotting functionality.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jason Galyardt
>>>>>> Department of Physics and Astronomy
>>>>>> University of Georgia
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>
> _______________________________________________
> 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/20150428/a433f87d/attachment.htm>
-------------- next part --------------
_______________________________________________
yt-users mailing list
yt-users at lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
More information about the yt-users
mailing list