[yt-users] Slice Plot Gadget Problem

[Gabriel Altay]

I'm not sure if this is the main cause of the problem, but the units for
that simulation should be kpc/h not Mpc/h.  It looks like yt is assuming
the box is 50,000 Mpc/h on a side.  You can set the units in the
yt.GadgetDataset command (
http://yt-project.org/doc/examining/loading_data.html?highlight=gadget#units-and-bounding-boxes).
  Try something like this,

ds = GadgetDataset("snap_005",
        unit_base = {'length': ('kpccm/h', 1.0)})

best,
-Gabriel



On Fri, Aug 8, 2014 at 12:39 PM, Jared Coughlin <Jared.W.Coughlin.29 at nd.edu>
wrote:

> Hi Nathan,
> Thank you for responding! I tried what you suggested, but still no luck.
> I'm still getting the index out of bounds error.  I've copied the traceback
> to the paste bin at: http://paste.yt-project.org/show/5001/
> I've included how I loaded the snapshot as well as the call to
> yt.SlicePlot, in case that helps.  Thank you very much for all the help!
> -Jared
>
>
> On Thu, Aug 7, 2014 at 5:12 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Jared,
>>
>> Try instead:
>>
>> yt.SlicePlot(ds, 'z', ('gas', 'density'), width=(10000., 'kpc'), center
>> ='m')
>>
>> (note the lower-case).
>>
>> ('Gas', 'Density') is a particle field, i.e. the Density values
>> associated with each of the Gas particles in your simulation.  ('gas',
>> 'density') is a mesh field - for SPH it is the smoothed gas density, taken
>> from the original Gas particles.  Particle fields are unstructured, the
>> field is only defined at the positions where particles exist.  Mesh fields
>> are defined over the whole simulation domain.
>>
>> Unfortunately there's some name collision here for gadget binary files so
>> I can see how this is confusing.  At the very least we should catch that
>> you're trying to create a SlicePlot of a particle field and crash with a
>> nicer, more understandable error.
>>
>> More detail on the difference between particle and mesh fields as well as
>> fields in yt in general here:
>> http://yt-project.org/docs/3.0/analyzing/fields.html
>>
>> Hope that helps,
>>
>> -Nathan
>>
>>
>> On Thu, Aug 7, 2014 at 2:08 PM, Jared Coughlin <
>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>
>>> Hi Nathan, I pasted the traceback here:
>>> http://paste.yt-project.org/show/4998/
>>> -Jared
>>>
>>>
>>> On Thu, Aug 7, 2014 at 4:16 PM, Jared Coughlin <
>>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>>
>>>> Hello! I have a vanilla gadget snapshot (one from the lcdm sample run
>>>> that the code comes with) that  I was able to plot by following the
>>>> instructions given here:
>>>>
>>>> http://yt-project.org/docs/3.0/cookbook/tipsy_notebook.html#tipsy-notebook
>>>>
>>>> I then moved on to the 'Making Smoothed Images' section of that page
>>>> and tried the SlicePlot command.  However, I get the following error:
>>>> IndexError: index 32767 is out of bounds for axis 0 with size 32767
>>>>
>>>> Basically, I'm not really sure what that means.  It seems like it's
>>>> overstepping the bounds of an array, as, for a zero-indexed array of size
>>>> 32767, index 32767 would be out of bounds by one.  I just wanted to see if
>>>> anyone else has had this problem, and if so, how they fixed it? Thank you
>>>> very much!
>>>>  -Jared
>>>>
>>>
>>>
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-- 
-- 
Gabriel Altay, PhD
Center for Relativistic Astrophysics
Georgia Institute of Technology, Physics Department
837 State Street, Atlanta, GA, 30332
phone: +01 404 205 9795
url: http://cosmo.gatech.edu/?page_id=1075
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