[yt-users] Analyzing SPH data

Nathan Goldbaum nathan12343 at gmail.com
Sat Mar 4 09:41:33 PST 2017


Oops, typo, should be https://bitbucket.org/ngoldbaum/yt


On Sat, Mar 4, 2017 at 11:40 AM Alankar Dutta <dutta.alankar at gmail.com>
wrote:

> 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/3eca2ae80ab14a48b643d3055d7d3c0933fa77ae/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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