[yt-users] Analyzing SPH data
Alankar Dutta
dutta.alankar at gmail.com
Sat Mar 4 09:40:07 PST 2017
Hello,
$ hg pull -r f4c5c13 https://bitbucket.org/yt_analysis/yt
This is giving the following error:
pulling from https://bitbucket.org/yt_analysis/yt
abort: unknown revision 'f4c5c13'!
Alankar Dutta
On Sat, Mar 4, 2017 at 10:46 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> To test my pull request you're going to want to build yt from a clone of
> the mercurial repository after pulling in my changes.
>
> $ conda uninstall yt
> $ hg clone https://bitbucket.org/yt_analysis/yt
> $ cd yt
> $ hg pull -r f4c5c13 https://bitbucket.org/yt_analysis/yt
> $ hg update f4c5c13
> $ python setup.py develop
>
> You'll need a compilation environment set up for that to succeed. If you
> don't have compilers installed it will be less straightforward to test
> this. I'd urge you *not* to hand-edit your installed version of yt from
> conda, as that will create more headaches for you if you make a mistake and
> forget to correct it.
>
>
> On Sat, Mar 4, 2017 at 10:34 AM Alankar Dutta <dutta.alankar at gmail.com>
> wrote:
>
>> 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/3eca2ae80ab14a48b643d3055d7d3c
>> 0933fa77ae/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
>>
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