[yt-users] Confused about units in derived fields

Naiman, Jill jill.naiman at cfa.harvard.edu
Fri Nov 21 10:30:30 PST 2014 

Ok!  Seems to work!  Thanks Nathan!

On Thu, Nov 20, 2014 at 10:38 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Thu, Nov 20, 2014 at 7:13 PM, Naiman, Jill <jill.naiman at cfa.harvard.edu
> > wrote:
>
>>
>>
>> On Thu, Nov 20, 2014 at 9:36 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hi Jill,
>>>
>>> On Thu, Nov 20, 2014 at 6:27 PM, Jill Naiman <
>>> jill.naiman at cfa.harvard.edu> wrote:
>>>
>>>> Hi all,
>>>>
>>>> As the title states, I am confused - specifically about units.  I want
>>>> to create a derived field where parts of the field are different values,
>>>> dependent upon some cutoff criteria like so:
>>>>
>>>> def _dene2(field,data):
>>>>     tl = data['temperature']
>>>>     dl = data['density']
>>>>     print("TEMP")
>>>>     print(tl.in_cgs())
>>>>     aux = np.where(tl.in_cgs() > 5000.)
>>>>     np.putmask(dl,aux, 0.0)
>>>>     dene = dl
>>>>     return dene
>>>>
>>>>
>>>> ds.add_field("dene", units="g/cm**3", function = _dene2)
>>>>
>>>>
>>>> Not only does this produce a very worrisome error:  "RuntimeError:
>>>> Something has gone terribly wrong, _function is NullFunc for ('flash',
>>>> 'temp')"
>>>>
>>>
>>> This happens when field detection fails badly.  I'm a bit surprised to
>>> see it referencing a "temp" field - have you defined a "temp" field
>>> somewhere?
>>>
>>
>> I do not have a "temp" field defined anywhere, its actually one of the
>> flash fields that is read in (I've printed out ds.field_list just to be
>> sure and see: [('flash', 'dens'), ('flash', 'temp'), ('flash', 'pres'),
>> ('flash', 'gpot'), ('flash', 'divb'), ('flash', 'velx'), ('flash', 'vely'),
>> ('flash', 'velz'), ('flash', 'magx'), ('flash', 'magy'), ('flash', 'magz'),
>> ('flash', 'magp')]
>>
>> ... I assume ('flash','temp') is 'temp'... or I am even more confused
>> than previously thought :)
>>
>>
>>
>>>
>>>
>>>>
>>>> The print statement in there shows a bunch of values close to 1, which
>>>> is why the "aux" mask never returns anything.But why is data a bunch of 1's
>>>> in here?  How do I access/convert to the "real" units?
>>>>
>>>
>>> yt's field detection algorithm will feed a field fake data that is close
>>> to 1 to see if there are errors in the field definition.  The values close
>>> to 1 you are seeing almost certainly come from field detection.  If the
>>> field validates correctly, real data will eventually be passed in.
>>>
>>
>> Makes sense, I assume in the actual plotting routine as that is where the
>> actual error is happening, full error below:
>>
>> Traceback (most recent call last):
>>   File "testderv.py", line 28, in <module>
>>     plot = yt.PhasePlot(my_sphere, "dene", "radius", ["temperature"],
>> weight_field="cell_volume")
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.py",
>> line 709, in __init__
>>     fractional=fractional)
>>   File "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
>> line 1151, in create_profile
>>     for f, l in zip(bin_fields, logs)]
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 483, in __call__
>>     rv = super(Extrema, self).__call__(fields, non_zero)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 59, in __call__
>>     sto.result = self.process_chunk(ds, *args, **kwargs)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py",
>> line 491, in process_chunk
>>     fd = data[field]
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 214, in __getitem__
>>     self.get_data(f)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 623, in get_data
>>     self._generate_fields(fields_to_generate)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 640, in _generate_fields
>>     fd = self._generate_field(field)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 251, in _generate_field
>>     tr = self._generate_fluid_field(field)
>>   File
>> "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 271, in _generate_fluid_field
>>     rv = finfo(gen_obj)
>>   File "/pfs/sw/yt-3.0/yt-x86_64/src/yt-hg/yt/fields/derived_field.py",
>> line 176, in __call__
>>     "for %s" % (self.name,))
>> RuntimeError: Something has gone terribly wrong, _function is NullFunc
>> for ('flash', 'temp')
>>
>>
>>>
>>> Is there any chance you can reproduce this issue using one of the test
>>> datasets on yt-project.org/data?  If so, can you pastebin a script that
>>> causes the error you're seeing?  That should make it much easier to
>>> reproduce and figure out exactly what's going wrong.
>>>
>>>
>> Done: http://paste.yt-project.org/show/5216/
>>
>
> When I phrase your script like this, it works for me:
>
> http://paste.yt-project.org/show/5217/
>
> I'm not sure why 'dene' is being associated with the flash field registry,
> but explicitly giving it a field type of 'gas' seems to work.
>
>
>> Thanks!
>> -Jill
>>
>>
>>> -Nathan
>>>
>>>
>>>>
>>>> Any help is appreciated,
>>>> -Jill
>>>>
>>>>
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