[yt-users] Saving and loading Arbitrary grid data

[Britton Smith]

Just to confirm, this is indeed that bug.  Qi, the error you showed is
exactly the issue that was fixed.

Britton

On Thu, Oct 19, 2017 at 10:08 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hi,
>
> I think this is due to a bug that was recently fixed by Britton Smith, see
> https://github.com/yt-project/yt/pull/1569. When I run your script using
> the current master branch in the yt git repository I don't see any errors.
>
> To get the fix right now you'll need to build the development version of
> yt from the git repository, see http://yt-project.org/docs/
> dev/installing.html#installing-yt-from-source
>
> We are probably overdue for a bugfix release so I've added an entry to my
> todo list to do the backports necessary to generate a bugfix release.
>
> Apologies for the trouble and thank you for the detailed report, hope
> that's helpful.
>
> -Nathan
>
> On Thu, Oct 19, 2017 at 4:35 PM, Li,Qi <pg3552 at ufl.edu> wrote:
>
>> Dear user group,
>>
>> I am trying to smooth particle data output from GIZMO onto an arbitrary
>> grid,  then save the object as data set  and reload in order to do volume
>> rendering. However I can not handle the reloaded data set.
>>
>> To clarify, I smooth yt sample data — FIRE_M12i_ref11 onto a 64**3 grid,
>> the code is like this:
>>
>>   1 import yt
>>   2
>>   3 ytname='FIRE_M12i_ref11/snapshot_600.hdf5'
>>   4 ds=yt.load(ytname)
>>   5
>>   6 # define the region
>>   7 left = ds.domain_left_edge
>>   8 right = ds.domain_right_edge
>>   9
>>  10 #now create an abitrary grid and save
>>  11 arb = ds.arbitrary_grid(left, right,dims=[64, 64, 64])
>>  12
>>  13 fn = arb.save_as_dataset(fields=[('PartType0','density')])
>>  14
>>  15 arb_ds = yt.load('snapshot_600_arbitrary_grid.h5')
>>  16 print arb_ds.field_list
>>
>> And it returns an error:
>>
>> Traceback (most recent call last):
>>   File "arbgrid_clean.py", line 16, in <module>
>>     * print arb_ds.field_list*
>>   ...
>>   ...
>>   File "/Users/heavyfat/anaconda/lib/python2.7/site-packages/yt/frontends/ytdata/io.py",
>> line 244, in _initialize_index
>>     pos[:,0] = _get_position_array(ptype, f, "x")
>> *ValueError: could not broadcast input array from shape (64,64,64) into
>> shape (262144)*
>>
>> So, how I can save/load a usable arbitrary grid dataset?
>> Thanks and looking forward to your suggestions.
>>
>> Best regards,
>> Qi
>>
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>>
>>
>
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