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

[Semyeong Oh]

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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