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

[Semyeong Oh]

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
>>>>>>
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>>>> --
>>>> Semyeong
>>>>
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>> --
>> Semyeong
>>
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-- 
Semyeong
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