[yt-users] Gadget snapshot read Problem
Jared Coughlin
Jared.W.Coughlin.29 at nd.edu
Tue Aug 18 15:39:24 PDT 2015
Great, thank you!
-Jared
On Tue, Aug 18, 2015 at 6:37 PM, Cameron Hummels <chummels at gmail.com> 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 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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