[yt-users] Particles in FLASH output
Jason Galyardt
jason.galyardt at gmail.com
Tue Apr 28 13:08:52 PDT 2015
Thanks, John. My domain size is 4 x 4 x 24 kpc, and the size of the
smallest cell is 31.25 pc, according to print_stats(). Here's the grid
info, in case it's useful:
level # grids # cells # cells^3
----------------------------------------------
0 48 24576 30
1 384 196608 59
2 3072 1572864 117
3 24448 12517376 233
----------------------------------------------
27952 14311424
Cheers,
Jason
On Tue, Apr 28, 2015 at 4:00 PM, John ZuHone <jzuhone at gmail.com> wrote:
> When I come back from the colloquium I will see what I can do with one of
> my own datasets.
>
> Jason, what is your domain size, and the size of the smallest cell?
>
> John ZuHone
> Kavli Center for Astrophysics and Space Research
> Massachusetts Institute of Technology
> 77 Massachusetts Ave., 37-582G
> Cambridge, MA 02139
> (w) 617-253-2354
> (m) 781-708-5004
> jzuhone at space.mit.edu
> jzuhone at gmail.com
> http://www.jzuhone.com
>
> On Apr 28, 2015, at 3:55 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> We have several public FLASH test datasets here:
>
> http://yt-project.org/data/
>
> I'm not sure whether any of them have both gas and particles.
>
> If you're ok with it and your dataset isn't enormous, it might help to
> share one of the data files you're working with. We've used dropbox or
> google drive to share big files on the mailing list in the past.
>
> On Tue, Apr 28, 2015 at 12:52 PM, Jason Galyardt <jason.galyardt at gmail.com
> > wrote:
>
>> 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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>>>>>>
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