[yt-users] clump as container

[Nathan Goldbaum]

On Tue, Dec 16, 2014 at 2:32 PM, David Collins <dcollins4096 at gmail.com>
wrote:
>
> Hi there--
>
> 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
> >>> leaf_clumps[n]['density']
> I get something sensical.  But if I do
> >>> leaf_clumps[n]['cell_mass']
> 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.
> >>> 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.
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141216/8ea79f72/attachment.htm>
-------------- next part --------------
_______________________________________________
yt-users mailing list
yt-users at lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org