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

[Semyeong Oh]

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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