[yt-users] Particles in FLASH output

Jason Galyardt jason.galyardt at gmail.com
Tue Apr 28 12:52:19 PDT 2015


Hi John,

It sounds like we have a bug in v3.0.2. But it's still not working in
v3.2dev. Do you have any test data that you can use to confirm? I would
just like to make sure it's not user error before I submit a bug report.

By the way, my output files seem fine - I can plot both gas density and
particle locations simultaneously in VisIt.

Cheers,
Jason

On Tue, Apr 28, 2015 at 3:44 PM, John Zuhone <jzuhone at gmail.com> wrote:

> The reason why this would not work in previous yt versions is that
> annotate_particles assumed code units for length, which for flash are
> centimeters. So “4" would be 4 cm, a ridiculously thin slab, which would
> explain why you end up with a zero selection.
>
> It should work now, based on looking at the code, so if it doesn’t then we
> definitely have a bug.
>
> On Apr 28, 2015, at 3:37 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>
>
> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
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