[yt-users] clump as container
David Collins
dcollins4096 at gmail.com
Thu Dec 18 07:15:20 PST 2014
>
> Yes -- although that behavior was also true in 2.x, to my recollection.
>
It definitely was, I did it a bunch-- I didn't understand the results I was
getting, so I didn't publish them yet. Now I think I do, and was hoping to
resume that work, so I'm definitely hoping to be able to get particles from
clumps soon.
> However, in 3.0, we *can* do this with a little bit of development, so
>
If you point me at some source, I'm happy to get started on that. All my
particles are massless, so the deposited mass isn't enough.
Thanks!
> I think on the whole it's a net win. With the work Doug Rudd did on
> composable objects, we should be able to supply one object as a
> base_source to another and then select particles that reside inside
> the cells that are selected, using bbox selection based on cells.
>
> All of that being said, I'd say just use the deposited mass from
> particles. It'll give you exactly the same result and will work with
> clumps. This was not available in 2.x, and now is in 3.x.
>
> Also, what I was alluding to in a previous email is that there's an
> internal "state" affiliated with an object -- "GenerationInProgress"
> -- which can sometimes, if an error is not correctly caught, be
> propagated up to the top. I think this is what's happening. Without
> it getting reset internally, it breaks the object.
>
> -Matt
>
> On Thu, Dec 18, 2014 at 8:57 AM, Britton Smith <brittonsmith at gmail.com>
> wrote:
> > 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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> >>> >>> --
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> >>> >>
> >>> >>
> >>> >>
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