[yt-users] Particles in FLASH output
Nathan Goldbaum
nathan12343 at gmail.com
Tue Apr 28 11:59:59 PDT 2015
There are instructions to switch to the development version here:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-from-source
On Tue, Apr 28, 2015 at 11:56 AM, 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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>>
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