[yt-users] Gadget snapshot read Problem
Matthew Turk
matthewturk at gmail.com
Wed Aug 19 09:35:49 PDT 2015
Hi Jared,
I think "show" will only work in the notebook. You'll have to call
pz.save() to save it to a file to view it if you're on the terminal.
-Matt
On Wed, Aug 19, 2015 at 11:34 AM, Jared Coughlin <Jared.W.Coughlin.29 at nd.edu
> wrote:
> Awesome, thanks, that worked like a charm! Just another quick question, if
> you wouldn't mind? I'm trying to make a simple projection plot from within
> ipython (terminal version, not the ipython notebook). I have all of my
> commands in a script that I run via: %run yt_script.py
>
> The script imports yt, numpy as np, pylab, and yt.units as units. It then
> loads the snapshot using ds = yt.GadgetDataset(fname, unit_base=unit_base,
> field_spec=my_field_def), does the indexing as ds.index, and then sets up a
> projection plot as: pz = yt.ProjectionPlot(ds, 'z', ('gas', 'density')).
> However, when I call pz.show(), I get this in my terminal:
>
> yt : [INFO ] 2015-08-19 12:26:28,544 Projection completed
> yt : [INFO ] 2015-08-19 12:26:28,544 xlim = 0.000000 50000.000000
> yt : [INFO ] 2015-08-19 12:26:28,544 ylim = 0.000000 50000.000000
> yt : [INFO ] 2015-08-19 12:26:28,546 xlim = 0.000000 50000.000000
> yt : [INFO ] 2015-08-19 12:26:28,546 ylim = 0.000000 50000.000000
> yt : [INFO ] 2015-08-19 12:26:28,552 Making a fixed resolution buffer
> of (('gas', 'density')) 800 by 800
> <yt.visualization.plot_window.ProjectionPlot at 0x7f01c5170850>
>
> And the plot does not actually show up anywhere. Do I have to manually
> set a graphics device/window or some such thing like you do in gnuplot, or
> am I missing a needed library that's causing the plot to not actually show
> up? Thanks, and sorry for the bother!
> -Jared
>
> On Tue, Aug 18, 2015 at 6:39 PM, Cameron Hummels <chummels at gmail.com>
> wrote:
>
>> Nathan is right. If you want to permanently add your field spec to the
>> codebase in the same way that I added the group0000 field spec, then you
>> (and your group) wouldn't need to define it in each script you're using.
>> To add it, you can put it in:
>>
>> yt/frontends/gadget/definitions.py, and just name it group0001.
>>
>> Let us know if you have any problems!
>>
>> Cameron
>>
>> On Tue, Aug 18, 2015 at 3:35 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Tue, Aug 18, 2015 at 5:28 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?
>>>>
>>>
>>> Yes, I think that's correct. It seems to be used that way in the
>>> group0000 field spec we have already. I've never actually tried to do what
>>> you're doing, though.
>>>
>>> By the way, if you *do* get this working, we'd love to include your
>>> field spec in yt itself so future users who have data that looks like yours
>>> won't have to deal with this. Unfortunately due to the proliferation of
>>> Gadget output types, someone at some point needs to add support for each
>>> custom type to yt so we can ascribe semantic meaning to all of the fields.
>>>
>>>
>>>> Also, here's the documentation page I was following:
>>>>
>>>> http://yt-project.org/doc/examining/loading_data.html?highlight=gadget_field_specs#gadget-data
>>>>
>>>
>>> I've issued a pull request to fix this here:
>>>
>>>
>>> https://bitbucket.org/yt_analysis/yt/pull-requests/1706/correcting-two-incorrect-paths-in-the/diff
>>>
>>>
>>>>
>>>>
>>>> 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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>>>>>> yt-users at lists.spacepope.org
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>>>>>>
>>>>>>
>>>>>
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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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