[yt-users] Gadget snapshot read Problem
Cameron Hummels
chummels at gmail.com
Tue Aug 18 15:37:02 PDT 2015
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 at 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_specs#gadget-data
>
> Thanks!
> -Jared
>
>
> On Tue, Aug 18, 2015 at 5:51 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> 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 It looks like you're reading some out of date documentation.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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--
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
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