[yt-users] Particles in FLASH output

John Zuhone jzuhone at gmail.com
Tue Apr 28 16:04:55 PDT 2015


Hmm, odd. 

At this point the best suggestion is Nathan’s—if you are able to post your dataset somewhere for us to look at, that would be helpful.

You can shoot me private mail at jzuhone at gmail.com if you don’t want it to go out to the whole list.

Best,

John

> On Apr 28, 2015, at 6:28 PM, Jason Galyardt <jason.galyardt at gmail.com> wrote:
> 
> Hi John,
> 
> There is no traceback; it fails silently.
> 
> Jason
> 
> On Apr 28, 2015 5:37 PM, "John Zuhone" <jzuhone at gmail.com <mailto:jzuhone at gmail.com>> wrote:
> Jason,
> 
> What is your traceback now? I’m also getting a failure over here but I want to check it against yours. 
> 
> Best,
> 
> John
> 
>> On Apr 28, 2015, at 4:08 PM, Jason Galyardt <jason.galyardt at gmail.com <mailto:jason.galyardt at gmail.com>> wrote:
>> 
>> 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 <mailto: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 <tel:617-253-2354>
>> (m) 781-708-5004 <tel:781-708-5004>
>> jzuhone at space.mit.edu <mailto:jzuhone at space.mit.edu>
>> jzuhone at gmail.com <mailto:jzuhone at gmail.com>
>> http://www.jzuhone.com <http://www.jzuhone.com/>
>> 
>> On Apr 28, 2015, at 3:55 PM, Nathan Goldbaum <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
>> 
>>> We have several public FLASH test datasets here:
>>> 
>>> http://yt-project.org/data/ <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 <mailto: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 <mailto: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 <mailto: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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