[yt-users] reading gadget-2 binary/hdf5 format

[Nathan Goldbaum]

Hi Semyeong,

I'm not able to reproduce this behavior in yt 3.3dev. Any chance you can
share what yt version you're using? The output of "yt version", run from
the command line, should be sufficient.

-Nathan

On Tue, May 3, 2016 at 11:06 AM, Semyeong Oh <semyeong.oh at gmail.com> wrote:

> Sure, this is the link http://use.yt/upload/28d51f76
>
> Semyeong
>
> On Tue, May 3, 2016 at 12:05 PM Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Any chance you can link to the HDF5 file? I don't have a gadget
>> development environment set up.
>>
>> You can use the yt curldrop:
>>
>> $ curl -T snapshot_000.hdf5 http://use.yt/upload/
>>
>> And then share the link this prints out here.
>>
>> -Nathan
>>
>> On Tue, May 3, 2016 at 11:02 AM, Semyeong Oh <semyeong.oh at gmail.com>
>> wrote:
>>
>>> Hi Nathan,
>>>
>>> The dataset is just from
>>> http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-2.0.7.tar.gz ICs/gassphere_littleendian.dat,
>>> and output from running the simulation
>>> (using /Gadget2/parameterfiles/gassphere.{Makefile/param} with format=2
>>> (hdf5)
>>>
>>> Semyeong
>>>
>>> On Tue, May 3, 2016 at 11:54 AM Matthew Turk <matthewturk at gmail.com>
>>> wrote:
>>>
>>>> Hi Semyeong,
>>>>
>>>> Looks like the bounding box is getting confused somehow, and it's
>>>> seeing it as the same value for left/right edge.  I think your ordering of
>>>> the bbox is correct (if it weren't, then changing the ordering to be
>>>> [[-bbox_lim, -bbox_lim, -bbox_lim], [bbox_lim, bbox_lim, bbox_lim]] would
>>>> fix it) but I'm not sure why it's failing.
>>>>
>>>> On Tue, May 3, 2016 at 10:46 AM, Semyeong Oh <semyeong.oh at gmail.com>
>>>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I'm having trouble reading gadget-2 both binary and hdf5 format, and
>>>>> was wondering if I could get some help.
>>>>> I'm testing out with the example distributed with gadget code, the gas
>>>>> sphere example which only
>>>>> contains ~1500 gas particles.
>>>>>
>>>>> - If I try to read the initial condition (distributed with gadget)
>>>>> binary file with yt.load, this command seems to
>>>>> execute fine, but the field_list returns empty list.
>>>>>
>>>>> - If I try to read the output of the simulation in hdf5 format,
>>>>> fname = 'output/snapshot_000.hdf5'
>>>>> unit_base = {'UnitLength_in_cm'         : 1.,
>>>>>              'UnitMass_in_g'            : 1.,
>>>>>              'UnitVelocity_in_cm_per_s' : 1.}
>>>>>
>>>>> bbox_lim = 5
>>>>> bbox = [[-bbox_lim,bbox_lim],
>>>>>         [-bbox_lim,bbox_lim],
>>>>>         [-bbox_lim,bbox_lim]]
>>>>>
>>>>> ds = yt.load(fname,unit_base=unit_base, bounding_box=bbox)
>>>>>
>>>>> and try ds.field_list or ds.print_stats,
>>>>> I end up getting something like this
>>>>> https://gist.github.com/smoh/7779e9ef546f9b05565aef86893dccd2
>>>>> which is obscure.
>>>>>
>>>>> What am I doing wrong?
>>>>>
>>>>> Thanks,
>>>>> Semyeong
>>>>> --
>>>>> Semyeong
>>>>>
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>>> --
>>> Semyeong
>>>
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> --
> Semyeong
>
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