[yt-users] problem with processing BoxLib data in pure hydro case

[Michael Zingale]

here's the PR:

https://bitbucket.org/yt_analysis/yt/pull-requests/2571/add-support-for-nyx-datasets-without/diff

On Mon, Apr 3, 2017 at 9:46 AM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> it looks like a lot of that logic changed in the latest dev version of yt,
> but there is still an issue reading Nyx datasets without particles.  I'll
> issue a PR to fix this on the dev version in a few minutes.
>
> On Mon, Apr 3, 2017 at 7:53 AM, Wolfram Schmidt <
> wolfram.schmidt at uni-hamburg.de> wrote:
>
>> Hi,
>>
>> I encountered a problem when processing BoxLib (Nyx) data from pure hydro
>> simulations without particles, using an Anaconda installation of yt.
>>
>> After loading a dataset with yt.load(), I get the following error for
>> ds.field_list:
>>
>> ---------------------------------------------------------------------------KeyError                                  Traceback (most recent call last)<ipython-input-5-5aaf470c0415> in <module>()----> 1 ds.field_list
>> /sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/data_objects/static_output.py in field_list(self)    459     @property    460     def field_list(self):--> 461         return self.index.field_list    462     463     def create_field_info(self):
>> /sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/data_objects/static_output.py in index(self)    417                 raise RuntimeError("You should not instantiate Dataset.")    418             self._instantiated_index = self._index_class(--> 419                 self, dataset_type=self.dataset_type)    420             # Now we do things that we need an instantiated index for    421             # ...first off, we create our field_info now.
>> /sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/frontends/boxlib/data_structures.py in __init__(self, ds, dataset_type)    906     def __init__(self, ds, dataset_type='nyx_native'):    907         super(NyxHierarchy, self).__init__(ds, dataset_type)--> 908         self._read_particle_header()    909     910     def _read_particle_header(self):
>> /sw/tools/anaconda3/4.1.1/generic/lib/python3.5/site-packages/yt/frontends/boxlib/data_structures.py in _read_particle_header(self)    909     910     def _read_particle_header(self):--> 911         if not self.ds.parameters["particles"]:    912             self.pgrid_info = np.zeros((self.num_grids, 3), dtype='int64')    913             return
>> KeyError: 'particles'
>>
>> Same problem with slices. I am not sure what exactly causes the error
>> here, but since I can load datasets from cosmological simulations with Nyx
>> and process them without problems, I suppose the problem outlined above is
>> somehow related to the missing particles.
>>
>> How can this be fixed?
>>
>> Best
>> Wolfram
>>
>>
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>>
>>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
> 11794-3800
> *phone*:  631-632-8225 <(631)%20632-8225>
> *e-mail*: Michael.Zingale at stonybrook.edu
> *web*: http://www.astro.sunysb.edu/mzingale
> github: http://github.com/zingale
>
>


-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
github: http://github.com/zingale
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