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

[Nathan Goldbaum]

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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