[yt-users] Gadget snapshot read Problem

[Jared Coughlin]

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 It looks like you're reading some out of date documentation.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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