I believe what's going on is that the object gets stuck in a mid-state
of generating data and is locked.  This is something that is not
supposed to happen, but we should be able to fail more gracefully.


Is it stuck because it's hard to get particles directly from the clump?  

 
> For now, a workaround would be to avoid using the total_mass derived
> quantity and instead do something like this:
>
> clump = ...
> total_mass = clump.quantity.total_quantity('cell_mass')
> clump['density']
> clump['cell_mass']
>
>>
>>
>> The curious disappearing data can be seen here:
>>
>> >>> leaf_clumps[0]['density']
>> YTArray([  94330.76550569,  111095.42419888,  111000.87780872,
>>         158489.47273191,  114487.69237444,  129849.08390983,
>>          95651.97426045,   95462.47824957,  104785.15137116,
>>         149758.92528478,  122558.83598019,   91829.8174425 ,
>>          97015.49553846,  118157.84068288]) g/cm**3
>> >>> leaf_clumps[0]['cell_mass']
>> YTArray([ 0.00070282,  0.00082773,  0.00082702,  0.00118084,  0.000853  ,
>>         0.00096745,  0.00071266,  0.00071125,  0.00078071,  0.00111579,
>>         0.00091313,  0.00068419,  0.00072282,  0.00088034]) g
>> >>> leaf_clumps[0].quantities.total_quantity('cell_mass')
>> 0.0118797558199 g
>> >>> leaf_clumps[0].quantities.total_mass()
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 193, in __call__
>>     rv = super(TotalMass, self).__call__(fields)
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 160, in __call__
>>     rv = super(TotalQuantity, self).__call__(fields)
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 56, in __call__
>>     sto.result = self.process_chunk(ds, *args, **kwargs)
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 166, in process_chunk
>>     for field in fields]
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py",
>> line 248, in __getitem__
>>     self.get_data(f)
>>   File
>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/selection_data_containers.py",
>> line 749, in get_data
>>     raise YTMixedCutRegion(self.conditionals, field)
>> yt.utilities.exceptions.YTMixedCutRegion: Can't mix particle/discrete and
>> fluid/mesh conditions or
>>                quantities.  Field: ('all', 'particle_mass') and Conditions
>> specified:
>>             obj['contours_72e8d63701e04d13bfec60cada79b7ad'] == 1
>> >>> leaf_clumps[0].quantities.total_quantity('cell_mass')
>> 0.0 g
>> >>> leaf_clumps[0]['cell_mass']
>> YTArray([], dtype=float64) g
>>
>>
>>
>> The code to make the clumps
>>
>>     ds = yt.load(setname)
>>     val, loc = ds.find_max('density')
>>     width = (0.05,'code_length')
>>     sphere = ds.sphere(loc,width)
>>     master_clump = Clump(sphere,"density")
>>     c_min = sphere["gas", "density"].min()
>>     c_max = sphere["gas", "density"].max()
>>     step = 2.0
>>     find_clumps(master_clump, c_min, c_max, step)
>>     leaf_clumps = get_lowest_clumps(master_clump)
>>
>>
>>>
>>> I'll give that a shot in the morning and report back.
>>>
>>>
>>> Thanks!
>>> d.
>>>
>>>>
>>>>
>>>>>
>>>>>
>>>>> If I instead try quantities.total_mass(), I get an odd error.
>>>>> >>> leaf_clumps[22].quantities.total_mass()
>>>>> Traceback (most recent call last):
>>>>>   File "<stdin>", line 1, in <module>
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>>>>> line 193, in __call__
>>>>>     rv = super(TotalMass, self).__call__(fields)
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>>>>> line 160, in __call__
>>>>>     rv = super(TotalQuantity, self).__call__(fields)
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>>>>> line 56, in __call__
>>>>>     sto.result = self.process_chunk(ds, *args, **kwargs)
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/derived_quantities.py",
>>>>> line 166, in process_chunk
>>>>>     for field in fields]
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py",
>>>>> line 248, in __getitem__
>>>>>     self.get_data(f)
>>>>>   File
>>>>> "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/selection_data_containers.py",
>>>>> line 749, in get_data
>>>>>     raise YTMixedCutRegion(self.conditionals, field)
>>>>> yt.utilities.exceptions.YTMixedCutRegion: Can't mix particle/discrete
>>>>> and fluid/mesh conditions or
>>>>>                quantities.  Field: ('all', 'particle_mass') and
>>>>> Conditions specified:
>>>>>             obj['contours_8d0408a91fc34e2bbe9eb838d48de46e'] == 1
>>>>
>>>>
>>>> This is happening because, as the error indicates, you can't combine
>>>> mesh and particle quantities in a cut_region (like a clump is).  The
>>>> total_mass() quantity returns the total mass in particles and gas, so that's
>>>> what's triggering the error. I bet this would work if you asked for the
>>>> total gas mass only. Of course, that would only work if clump['cell_mass']
>>>> returned something sensible.
>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I build the clumps in the following manner.  I don't have any
>>>>> validators by design.  Plotting the clumps with annotate_clumps(leaf_clumps)
>>>>> gives reasonable results.
>>>>>
>>>>>     ds = yt.load(setname)
>>>>>     loc = ds.arr([ 0.03613281,  0.79589844,  0.03027344],
>>>>> 'code_length')
>>>>>     width = (0.05,'code_length')
>>>>>     sphere = ds.sphere(loc,width)
>>>>>     master_clump = Clump(sphere,"density")
>>>>> use_particles=False, use_thermal_energy=False)
>>>>>     c_min = sphere["gas", "density"].min()
>>>>>     c_max = sphere["gas", "density"].max()
>>>>>     step = 2.0
>>>>>     find_clumps(master_clump, c_min, c_max, step)
>>>>>     leaf_clumps = get_lowest_clumps(master_clump)
>>>>>
>>>>> Thanks a ton!
>>>>> d.
>>>>>
>>>>> --
>>>>> -- Sent from a computer.
>>>>>
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>>
>>
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