[yt-users] Slice Plot Gadget Problem

Fri Aug 8 15:21:35 PDT 2014

No problem, thank you very much for all your help, I really appreciate it!
-Jared
On Aug 8, 2014 5:48 PM, "Nathan Goldbaum" <nathan12343 at gmail.com> wrote:

> 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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