[yt-users] Slice Plot Gadget Problem

[Jared Coughlin]

Hi,
I tried changing the units, and that gave the same error. I also tried
changing the center to 'c', and same thing.  I've posted the contents of
ds.field_list and ds.derived_field_list here:
http://paste.yt-project.org/show/5003/

The plot of ('deposit'', 'Gas_smoothed_Density') also didn't work.  The
traceback is here: http://paste.yt-project.org/show/5004/

The plot of ('deposit', 'all_cic') worked, however. At least, it ran and
produced an image without throwing any errors.  I can upload the image to
google drive, if you'd like?

As for the snapshot, it's not very big, only 2.2M.  I can put that on
google drive as well.  Also, it's little endian.  I can upload the
parameter file and ic file, as well, if you'd like.
-Jared




On Fri, Aug 8, 2014 at 1:51 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hi Jared,
>
> Looking at the traceback, it seems the issue is in calculating the maximum
> gas density in the simulation.  I'm not sure why this is failing, but to
> see if we can create a plot at all, can you try supplying 'c' as the plot
> center instead of 'm'?
>
> Can you also paste the contents of 'ds.field_list' and
> 'ds.derived_field_list'?
>
> Additionally, can you create a SlicePlot of one of the following fields:
>
> ('deposit', 'Gas_smoothed_Density')
> ('deposit', 'all_cic')
>
> The first is another name for the SPH smoothed gas density - I'm checking
> here whether the ('gas', 'density') alias is misbehaving.  The second is
> the cloud-in-cell deposited density for all particles in the simulation - I
> want to make sure that deposition isn't completely broken for your dataset.
>
> Lastly, if the dataset isn't enormous and it is ok to share it, it would
> be helpful if you could share the actual dataset so one of us can reproduce
> your problem locally.  We've had a lot of success using dropbox and google
> drive for this purpose in the past.
>
> Hopefully we'll be able to get to the bottom of this,
>
> Nathan
>
>
>
> On Fri, Aug 8, 2014 at 9:39 AM, 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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