[yt-users] particle smoothing bug in latest version of yt

[Matthew Turk]

Hi Desika,

I've issued a PR to alias "Metallicity" too.  That should fix it.

https://bitbucket.org/yt_analysis/yt/pull-request/904/adding-metallicity-for-sph-data/diff

-Matt

On Thu, May 15, 2014 at 6:59 AM, Desika Narayanan
<dnarayan at haverford.edu> wrote:
> Hey Matt,
>
> Thanks for looking into it - the field list is printed below
>
> (Pdb) pprint.pprint(sorted(pf.field_list))
>
> [('PartType0', 'Coordinates'),
>
>  ('PartType0', 'Density'),
>
>  ('PartType0', 'ElectronAbundance'),
>
>  ('PartType0', 'InternalEnergy'),
>
>  ('PartType0', 'Masses'),
>
>  ('PartType0', 'Metallicity'),
>
>  ('PartType0', 'NeutralHydrogenAbundance'),
>
>  ('PartType0', 'ParticleIDs'),
>
>  ('PartType0', 'Potential'),
>
>  ('PartType0', 'SmoothingLength'),
>
>  ('PartType0', 'StarFormationRate'),
>
>  ('PartType0', 'Velocities'),
>
>  ('PartType1', 'Coordinates'),
>
>  ('PartType1', 'Masses'),
>
>  ('PartType1', 'ParticleIDs'),
>
>  ('PartType1', 'Potential'),
>
>  ('PartType1', 'Velocities'),
>
>  ('PartType2', 'Coordinates'),
>
>  ('PartType2', 'Masses'),
>
>  ('PartType2', 'ParticleIDs'),
>
>  ('PartType2', 'Potential'),
>
>  ('PartType2', 'Velocities'),
>
>  ('PartType3', 'Coordinates'),
>
>  ('PartType3', 'Masses'),
>
>  ('PartType3', 'ParticleIDs'),
>
>  ('PartType3', 'Potential'),
>
>  ('PartType3', 'Velocities'),
>
>  ('PartType4', 'Coordinates'),
>
>  ('PartType4', 'Masses'),
>
>  ('PartType4', 'Metallicity'),
>
>  ('PartType4', 'ParticleIDs'),
>
>  ('PartType4', 'Potential'),
>
>  ('PartType4', 'StellarFormationTime'),
>
>  ('PartType4', 'Velocities'),
>
>  ('PartType5', 'BH_Mass'),
>
>  ('PartType5', 'BH_Mdot'),
>
>  ('PartType5', 'Coordinates'),
>
>  ('PartType5', 'Masses'),
>
>  ('PartType5', 'ParticleIDs'),
>
>  ('PartType5', 'Potential'),
>
>  ('PartType5', 'Velocities'),
>
>  ('all', 'Coordinates'),
>
>  ('all', 'Masses'),
>
>  ('all', 'ParticleIDs'),
>
>  ('all', 'Potential'),
>
>  ('all', 'Velocities')]
>
>
>
>
>
>
> On Thu, May 15, 2014 at 6:49 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> Hi Desika,
>>
>> Looks like a bug, yes.  I think the problem is that "metal_density" is
>> not getting aliased correctly for your dataset.  What is the output
>> of:
>>
>> import pprint
>> pprint.pprint(sorted(ds.field_list))
>>
>> where ds is your dataset.
>>
>> -Matt
>>
>> On Wed, May 14, 2014 at 9:05 AM, Desika Narayanan
>> <dnarayan at haverford.edu> wrote:
>> > Hi YT,
>> >
>> > I have a function that loads a pf from a Gadget data set, and then
>> > smooths a
>> > few physical quantities (gas metallicity; mass; density) onto an octree,
>> > and
>> > then returns them:
>> >
>> > http://paste.yt-project.org/show/4624/
>> >
>> > in an older version of yt (3.0) that I'm using: 7cf523a36d10 (yt-3.0)
>> >
>> > this works, no problem.  if I run yt-update, to get to:  4d1488b8fa47
>> >
>> > this gives the following traceback copied below.  Has something
>> > important
>> > changed that should affect the way I use smoothing functions?
>> >
>> > -desika
>> >
>> >
>> >
>> >
>> >   File "/Users/desika/Dropbox/powderday/particle_smooth_yt.py", line 41,
>> > in
>> > yt_smooth
>> >     saved["metallicity"] = ad["gas", "metallicity"]
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 214, in __getitem__
>> >     self.get_data(f)
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 623, in get_data
>> >     self._generate_fields(fields_to_generate)
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 640, in _generate_fields
>> >     fd = self._generate_field(field)
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 251, in _generate_field
>> >     tr = self._generate_fluid_field(field)
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 271, in _generate_fluid_field
>> >     rv = finfo(gen_obj)
>> >   File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/derived_field.py",
>> > line
>> > 178, in __call__
>> >     dd = self._function(self, data)
>> >   File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/fluid_fields.py",
>> > line
>> > 153, in _metallicity
>> >     tr = data[ftype, "metal_density"] / data[ftype, "density"]
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 207, in __getitem__
>> >     f = self._determine_fields([key])[0]
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> > line
>> > 455, in _determine_fields
>> >     finfo = self.pf._get_field_info(ftype, fname)
>> >   File
>> > "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
>> > line 487, in _get_field_info
>> >     raise YTFieldNotFound((ftype, fname), self)
>> > yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas',
>> > 'metal_density')' in snapshot_006.
>> >
>> >
>> >
>> >
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