[yt-users] Slice Plot Gadget Problem

[Matthew Turk]

Hi Jared,

I've found the bug and issued a fix, here:

https://bitbucket.org/yt_analysis/yt/pull-request/1140/adding-check-for-no-fields-ptypes-in/diff

Should go in shortly.  (I put up a projection just for fun.)

-Matt

On Fri, Aug 8, 2014 at 5:21 PM, Jared Coughlin
<Jared.W.Coughlin.29 at nd.edu> wrote:
> 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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