Re: [yt-users] Gadget snapshot read Problem

19 Aug 2015


      Great, thank you!
-Jared

On Tue, Aug 18, 2015 at 6:37 PM, Cameron Hummels  wrote:
...
Hey Jared,
Yeah, ("C", ("Gas", "Stars")) is the right syntax.  Good luck!
Cameron
On Tue, Aug 18, 2015 at 3:28 PM, Jared Coughlin <
Jared.W.Coughlin.29@nd.edu> wrote:
...
Thanks! I'll give that a try.  Also, in my field_spec definition, for
those fields that applied to more than one particle type, I edited it to
have () around them, so it reads ("C", ("Gas", "Stars")).  Is that the
right way to do that? Also, here's the documentation page I was following:
http://yt-project.org/doc/examining/loading_data.html?highlight=gadget_field...
Thanks!
-Jared
On Tue, Aug 18, 2015 at 5:51 PM, Nathan Goldbaum 
wrote:
...
On Tue, Aug 18, 2015 at 4:46 PM, Jared Coughlin <
Jared.W.Coughlin.29@nd.edu> wrote:
...
Hello! I have two questions: the first is related to saving new field
specs, and the second is related to reading in the file itself.
I was following along with the documentation that describes saving new
field specs, and I defined a new field spec as (it should be noted that my
extra columns are for both gas and star particles, and I was unsure as to
how to tell yt that it applied for both types, so I made a best guess):
my_field_def = ("Coordinates",
                  "Velocities",
                  "ParticleIDs",
                  "Mass",
                  ("InternalEnergy", "Gas"),
                  ("Density", "Gas"),
                  ("SmoothingLength", "Gas"),
                  ("RII", "Stars"),
                  ("RIa", "Stars"),
                  ("StellarAge", "Stars"),
                  ("C", "Gas", "Stars"),
                  ("O", "Gas", "Stars"),
                  ("Ca", "Gas", "Stars"),
                  ("Cr", "Gas", "Stars"),
                  ("Mn", "Gas", "Stars"),
                  ("Fe", "Gas", "Stars"),
               )
And a unit base:
unit_base = {'UnitLength_in_cm' : 3.085678e+21,
               'UnitMass_in_g' : 1.989e+43,
               'UnitVelocity_in_cm_per_s' : 1.0e+5}
Firstly, when I tried to add my custom field definition to the
gadget_field_specs by doing:
from yt.frontends.sph.definitions import gadget_field_specs
I get the error:
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named definitions
Just wondering what I was doing wrong?  Also, when I try to load in the
snapshot, I am doing:
It looks like you're reading some out of date documentation. The correct
import is now "from yt.frontends.gadget.definitions import
gadget_field_specs"
Can you paste the link to the page with the incorrect import? If it's
still that way in the latest version of the docs, we can correct it.
...
fname = 'snapshot_000.0'
ds = yt.GadgetDataset(fname, unit_base=unit_base,
field_spec=my_field_def)
ds.index
ad = ds.all_data()
pz = yt.ProjectionPlot(ds, 'z', ('gas', 'density'))
pz.show()
The output is:
yt : [INFO     ] 2015-08-18 17:24:45,103 Calculating time from
2.500e-01 to be 6.950e+16 seconds
yt : [INFO     ] 2015-08-18 17:24:45,144 Parameters: current_time
       = 6.95032608578e+16 s
yt : [INFO     ] 2015-08-18 17:24:45,144 Parameters: domain_dimensions
        = [2 2 2]
yt : [INFO     ] 2015-08-18 17:24:45,144 Parameters: domain_left_edge
       = [ 0.  0.  0.]
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters: domain_right_edge
        = [ 50000.  50000.  50000.]
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters:
cosmological_simulation   = 1
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters: current_redshift
       = 3.00000005201
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters: omega_lambda
       = 0.726
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters: omega_matter
       = 0.274
yt : [INFO     ] 2015-08-18 17:24:45,145 Parameters: hubble_constant
        = 0.702
yt : [INFO     ] 2015-08-18 17:24:45,146 Allocating for 4.194e+06
particles
yt : [INFO     ] 2015-08-18 17:24:45,664 Identified 3.077e+05 octs
Traceback (most recent call last):
  File "yt_test_script.py", line 72, in <module>
    ds.index
  File
"/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
line 321, in index
    self, dataset_type=self.dataset_type)
  File
"/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py",
line 53, in __init__
    super(ParticleIndex, self).__init__(ds, dataset_type)
  File
"/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py",
line 65, in __init__
    self._detect_output_fields()
  File
"/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/geometry/particle_geometry_handler.py",
line 125, in _detect_output_fields
    fl, _units = self.io._identify_fields(dom)
  File
"/home/user/Research/Tools/yt/yt-x86_64/src/yt-hg/yt/frontends/gadget/io.py",
line 208, in _identify_fields
    field, req = field
ValueError: too many values to unpack
This is probably related to not having the correct field spec when
loading the data.
...
The snapshot I'm trying to load is a 128^3 50Mpc snapshot distributed
onto 4 files and the error occurs on a call to ds.index, if that helps.
Thank you!
-Jared
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--
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
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