[yt-users] adding a smoothed field

Desika Narayanan dnarayan at haverford.edu
Tue Nov 11 06:22:49 PST 2014


Hey All,

Just for posterity, Matt suggested the following (offline) which worked. :

add_field(("PartType0","MetalDens"),function=_metaldens,units="g/cm**3")

to
add_field(("PartType0","MetalDens"),function=_metaldens,units="g/cm**3",
particle_type=True)


So, in summary, to add a smoothed field, the add_field command should be
called as above), followed by the adding of a
volume_weighted_smoothed_field via something like:
metal_field = add_volume_weighted_smoothed_field("PartType0",
"Coordinates", "Masses",
                                              "SmoothingLength",
"Density","MetalDens",
                                              ds.field_info)







On Mon, Nov 10, 2014 at 1:54 PM, Desika Narayanan <dnarayan at haverford.edu>
wrote:

> Hey Matt,
>
> Thanks for this!  This definitely added a field though has a small hiccup
> when trying to access the information in it.    I can't seem to access the
> yt pastebin, so I'll copy the issue below.
>
> #I define metaldens (metal density) as:
> def _metaldens(field,data): return
> (data["PartType0","Density"]*data["PartType0","Metallicity"])
>
> add_field(("PartType0","MetalDens"),function=_metaldens,units="g/cm**3"]
> ds = load(fname,unit_base=unit_base,bounding_box=bbox)
> ds.index
> ad = ds.all_data()
>
> #then add the smoothed field
> metal_fn = add_volume_weighted_smoothed_field("PartType0", "Coordinates",
> "Masses",
>                                               "SmoothingLength",
> "Density","MetalDens",
>                                               ds.field_info)
>
> metal_fn = metal_fn[0]
>
> #when trying to access this information, though, I get the error below:
> print ad[metal_fn]
>
>
>
> Traceback (most recent call last):
>
>   File "gadget_load.py", line 32, in <module>
>
>     print ad[metal_fn]
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 240, in __getitem__
>
>     self.get_data(f)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 661, 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 681, in _generate_fields
>
>     fd = self._generate_field(field)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 277, 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 295, in _generate_fluid_field
>
>     rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 311, in _generate_spatial_fluid
>
>     ind += o.select(self.selector, self[field], rv, ind)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 240, in __getitem__
>
>     self.get_data(f)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 661, 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 681, in _generate_fields
>
>     fd = self._generate_field(field)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 277, 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 297, in _generate_fluid_field
>
>     rv = finfo(gen_obj)
>
>   File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/derived_field.py",
> line 184, in __call__
>
>     dd = self._function(self, data)
>
>   File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/particle_fields.py",
> line 551, in _vol_weight
>
>     quan = data[ptype, smoothed_field].in_units(field_units)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/octree_subset.py", line
> 76, in __getitem__
>
>     tr = super(OctreeSubset, self).__getitem__(key)
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 233, in __getitem__
>
>     f = self._determine_fields([key])[0]
>
>   File
> "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 500, in _determine_fields
>
>     raise YTFieldTypeNotFound(ftype)
>
> yt.utilities.exceptions.YTFieldTypeNotFound: Could not find field
> 'PartType0'.
>
>
>
>
> On Mon, Nov 10, 2014 at 11:49 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
>
>> Hi Desika,
>>
>> Looking over the code, if you have a *particle* quantity, you should be
>> able to add a *smoothed* quantity using this type of construction:
>>
>> from yt.fields.particle_fields import add_volume_weighted_smoothed field
>>
>> The API for this function is:
>>
>> def add_volume_weighted_smoothed_field(ptype, coord_name, mass_name,
>>         smoothing_length_name, density_name, smoothed_field, registry,
>>         nneighbors = None)
>>
>> so you should be able to supply particle type, "particle_position",
>> "particle_mass", "smoothing_length", the density name ("density" probably),
>> the name of the field to smooth, and then the ds.field_info.  I believe
>> this should do it, and it may require another step but I don't think so.
>>
>> -Matt
>>
>> On Mon Nov 10 2014 at 8:22:08 AM Desika Narayanan <dnarayan at haverford.edu>
>> wrote:
>>
>>>
>>> Hey All,
>>>
>>> I'm trying to figure out how to add a new smoothed field to a data set.
>>> Specifically, I want to add a (particle) field, and then be able to access
>>> the smoothed mesh quantities (the same way I would access the mesh
>>> quantities of density as below, for example)
>>>
>>> ad = ds.all_data()
>>>
>>> ad["deposit","PartType0_smoothed_desnsity"]
>>>
>>> (in this case PartType0 is gas).   I'm adding a field prior to loading
>>> the data set as described here:
>>>
>>> http://yt-project.org/doc/developing/creating_derived_
>>> fields.html#defining-a-new-field
>>>
>>> thanks,
>>>
>>> desika
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
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>>
>>
>
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