[yt-users] Particles in FLASH output
John Zuhone
jzuhone at gmail.com
Tue Apr 28 12:44:37 PDT 2015
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 <mailto: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 <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 <mailto: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 <mailto: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 <http://g1.id/> - g1._id_offset]
> 73 end = p_ind[g2.id <http://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 <http://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 <mailto:nathan12343 at gmail.com>> wrote:
>
>
> On Tue, Apr 28, 2015 at 11:37 AM, Nathan Goldbaum <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
>
>
> On Tue, Apr 28, 2015 at 11:36 AM, Jason Galyardt <jason.galyardt at gmail.com <mailto: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
>
>
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