[yt-users] Gadget snapshot read Problem
Nathan Goldbaum
nathan12343 at gmail.com
Tue Aug 18 14:51:10 PDT 2015
On Tue, Aug 18, 2015 at 4:46 PM, Jared Coughlin <Jared.W.Coughlin.29 at 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It looks like you're reading some out of date documentation.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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>
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