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

[Nathan Goldbaum]

Hi Semyeong,

Hmm, so I just tried with yt 3.2.3, and I'm unable to reproduce this using
the following script (and with the snapshot you uploaded in the same
directory as the script):

http://paste.yt-project.org/show/6455/

So I'm not sure what's going wrong on your setup. Are you unable to run my
pasted script?

-Nathan

On Tue, May 3, 2016 at 11:13 AM, Semyeong Oh <semyeong.oh at gmail.com> wrote:

> It is
>
> yt module located at:
>     /Users/semyeong/miniconda2/envs/yt/lib/python2.7/site-packages
>
> The current version and changeset for the code is:
>
> ---
> Version = 3.2.3
> Changeset = None
> ---
>
> Semyeong
>
> On Tue, May 3, 2016 at 12:09 PM Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
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>>>>>>
>>>>> --
>>>>> Semyeong
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
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>>>>>
>>>>>
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>>> --
>>> Semyeong
>>>
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> --
> Semyeong
>
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