Re: [yt-users] adding a smoothed field

11 Nov 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 
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 
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 
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
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