[yt-users] clump as container

Britton Smith brittonsmith at gmail.com
Thu Dec 18 06:57:15 PST 2014 

My understanding is that in yt-3.0 we cannot get particles from clumps.  Is
that true?

On Thu, Dec 18, 2014 at 9:36 AM, David Collins <dcollins4096 at gmail.com>
wrote:
>
>
>> 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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>> >>>
>> >>>
>> >>> --
>> >>> -- Sent from a computer.
>> >>
>> >>
>> >>
>> >> --
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