On Tue, Dec 16, 2014 at 2:32 PM, David Collins email@example.com wrote:
I'm doing something wrong with clumps in yt3, and can't quite figure out what I"m doing. When I make some clumps, the field 'density' shows up, but no other fields seem to be well defined. Is this a familiar error to anyone? What I'm doing is the following:
I make some clumps from a sphere, similar to what's in the docs (details at the end of the email), and when I do
I get something sensical. But if I do
YTArray(, dtype=float64) g
I get this empty array.
Not sure why this is happening. Any chance you can reproduce it using one of the test datasets on yt-project.org/data?
If I instead try quantities.total_mass(), I get an odd error.
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.
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