On Wed Dec 17 2014 at 10:24:51 AM David Collins
Not sure why this is happening. Any chance you can reproduce it using one
of the test datasets on yt-project.org/data?
I tried with the IsolatedGalaxy simulation, using the same code as before (below for reference) but everything works fine.
I did learn that if I don't do quantities.total_mass() on any clump, I get sensical results, but as soon as I do call total_mass, it eliminates the data on all clumps. This simulation has only tracer particles, an no other particles, is that possibly the problem?
Ah, thanks for the hint, I can reproduce this using IsolatedGalaxy now. I will file an issue shortly. Having a repro script should help debugging here. 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.
> 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",
If I instead try quantities.total_mass(), I get an odd error. 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.
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