[yt-users] Analyzing SPH data

[Nathan Goldbaum]

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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>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
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