[yt-users] Slice Plot Gadget Problem

Fri Aug 8 14:48:03 PDT 2014

Ok, I can trigger the error you're seeing locally.  I've passed this on to
Matt who can take a closer look at what's happening and hopefully fix the
issue you're running into.

Sorry for the difficulties, hopefully we'll have this cleared up soon.
 Thanks also for reporting this and working with us.

On Fri, Aug 8, 2014 at 12:55 PM, Jared Coughlin <Jared.W.Coughlin.29 at nd.edu>
wrote:

> 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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