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?
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_chunkfor 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_dataraise YTMixedCutRegion(self.conditionals, field)yt.utilities.exceptions.YTMixedCutRegion: Can't mix particle/discrete and fluid/mesh conditions orquantities. 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) gThe code to make the clumpsds = 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 = 2.0find_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_chunkfor 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_dataraise YTMixedCutRegion(self.conditionals, field)yt.utilities.exceptions.YTMixedCutRegion: Can't mix particle/discrete and fluid/mesh conditions orquantities. Field: ('all', 'particle_mass') and Conditions specified:obj['contours_8d0408a91fc34e2bbe9eb838d48de46e'] == 1This 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 = 2.0find_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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