[yt-users] Analyzing SPH data
Alankar Dutta
dutta.alankar at gmail.com
Sat Mar 4 08:34:46 PST 2017
Hello,
I have modified the yt files as given in the pull request. I get the
following error code:
Traceback (most recent call last):
File "dev.py", line 9, in <module>
import yt
File
"/home/alankar/anaconda3/lib/python3.6/site-packages/yt/__init__.py", line
133, in <module>
frontends = _frontend_container()
File
"/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/api.py",
line 52, in __init__
setattr(self, frontend, importlib.import_module(_mod))
File "/home/alankar/anaconda3/lib/python3.6/importlib/__init__.py", line
126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File
"/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/eagle/api.py",
line 17, in <module>
from .data_structures import \
File
"/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/eagle/data_structures.py",
line 21, in <module>
from yt.frontends.gadget.data_structures import \
File
"/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/gadget/data_structures.py",
line 28, in <module>
from yt.frontends.sph.data_structures import \
ImportError: cannot import name 'SPHDataset'
The following is my code:
import yt
ds = yt.load("snapshot_068.0")
Alankar Dutta
On Sat, Mar 4, 2017 at 3:13 PM, Alankar Dutta <dutta.alankar at gmail.com>
wrote:
> Oh I missed telling that the full dataset is around 950 GB
>
> On Sat, Mar 4, 2017 at 1:02 PM, Alankar Dutta <dutta.alankar at gmail.com>
> wrote:
>
>> Hello,
>>
>> This is only one part of the multipart snapshot of the simulation. I am
>> sending you the header information from the snapshot file:
>>
>> {'O0': 0.27500000000000002,
>> 'Ol': 0.72499999999999998,
>> 'boxsize': 100000.0,
>> 'flag_age': 1,
>> 'flag_cooling': 1,
>> 'flag_delaytime': 0,
>> 'flag_fb': 1,
>> 'flag_fh2': 0,
>> 'flag_metals': 1,
>> 'flag_potential': 3,
>> 'flag_sfr': 1,
>> 'flag_tmax': 0,
>> 'h': 0.70199999999999996,
>> 'massTable': array([ 0. , 0.00110449, 0. , 0. , 0. , 0. ]),
>> 'nbndry': 76247,
>> 'nbulge': 0,
>> 'ndisk': 0,
>> 'ndm': 1459617792,
>> 'nfiles': 1024,
>> 'ngas': 1343721867,
>> 'npartThisFile': array([10045237, 10239661, 0, 0, 451148, 67], dtype=uint32),
>> 'npartTotal': array([1343721867, 1459617792, 0, 0, 503500456,
>> 76247], dtype=uint32),
>> 'npartTotalHW': array([1, 1, 0, 0, 0, 0], dtype=uint32),
>> 'nstar': 503500456,
>> 'redshift': 1.0000000010567627,
>> 'rhocrit': 2.707660428120944e-29,
>> 'time': 0.49999999973580939}
>>
>>
>>
>> I extracted this information using a different python program.
>>
>> Alankar Dutta
>>
>> On Sat, Mar 4, 2017 at 12:45 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Sat, Mar 4, 2017 at 12:25 AM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Sat, Mar 4, 2017 at 12:13 AM, Alankar Dutta <dutta.alankar at gmail.com
>>>> > wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Modifying the GADGET simulation isn't possible the moment because it
>>>>> has already been developed by someone else who has a paper published on
>>>>> this simulation and I want to use that simulation snapshots to make mock
>>>>> xray map from it.
>>>>>
>>>>
>>>> I'm talking about modifying yt, not Gadget.
>>>>
>>>> Is the file you attached to your other e-mail just a single file in a
>>>> multi-file dataset? How large is the full dataset? Do you not have a way to
>>>> produce a full dataset in this output format that's not prohibitively large?
>>>>
>>>
>>> I've opened a pull request that allows me to do IO on the data you
>>> attached: https://bitbucket.org/yt_analysis/yt/pull-requests/2537
>>>
>>> This allows me to read your data in, getting sensible values for e.g.
>>> position. I suspect we're not using the correct field specification because
>>> I see this warning:
>>>
>>> yt : [WARNING ] 2017-03-04 01:06:09,109 Your Gadget-2 file may have
>>> extra columns or different precision! (1814947576 file vs 1486279952
>>> computed)
>>>
>>> yt supports a number of field specifications out of the box, see:
>>>
>>> https://bitbucket.org/yt_analysis/yt/src/3eca2ae80ab14a48b64
>>> 3d3055d7d3c0933fa77ae/yt/frontends/gadget/definitions.py?at=
>>> yt&fileviewer=file-view-default#definitions.py-50
>>>
>>> Do you happen to know which fields are in your output file?
>>>
>>>
>>>>
>>>>
>>>>>
>>>>>
>>>>> Alankar Dutta
>>>>>
>>>>> On Mar 4, 2017 11:38 AM, "Nathan Goldbaum" <nathan12343 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> I think the most straightforward thing to do here is to fix the
>>>>>> Gadget frontend so it properly reads in gadget binary data with positions
>>>>>> written in double precision.
>>>>>>
>>>>>> Is there any chance you can generate a smallish test dataset in your
>>>>>> Gadget output format that we can use for debugging purposes? With that
>>>>>> available it should be straightforward to add support. You can share the
>>>>>> dataset using the yt curldrop (https://docs.hub.yt/services.
>>>>>> html#curldrop) or a cloud filesharing service like dropbox or google
>>>>>> drive.
>>>>>>
>>>>>> Unfortunately there isn't a way to load SPH data without a
>>>>>> full-fledged frontend right now.
>>>>>>
>>>>>> We do have a load_particles function which allows creating a dataset
>>>>>> from particle data loaded as numpy arrays, but it's currently not possible
>>>>>> to use it to load SPH data.
>>>>>>
>>>>>> I'm currently actively working on improving support for SPH data in
>>>>>> yt and adding the ability to load SPH data with load_particles is one of
>>>>>> the things I've added in that branch of the code. Hopefully this work will
>>>>>> be stabilized sometime in the next few months.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Mar 3, 2017 at 11:45 PM, Alankar Dutta <
>>>>>> dutta.alankar at gmail.com> wrote:
>>>>>>
>>>>>>> Hello yt-community,
>>>>>>>
>>>>>>> I am a beginner on yt. I have an array of data which I have read
>>>>>>> from a Gadget simulation snapshot. It is not directly supported by yt at
>>>>>>> present (I have ensured this by already discussing this issue in the
>>>>>>> community before). The array has position,velocity, density, mass, internal
>>>>>>> energy and smoothing length information on the gas particles. Now how can I
>>>>>>> use this to make the slice plots or other useful visualizations?
>>>>>>>
>>>>>>> Alankar Dutta,
>>>>>>> Third year Undergraduate,
>>>>>>> Physics Department,
>>>>>>> Presidency University, India
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
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>>>>
>>>
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>>
>
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