[yt-users] yt basic visualization for gadget output

Junhwan Choi (최준환) choi.junhwan at gmail.com
Sat Dec 13 22:20:56 PST 2014


On Sat, Dec 13, 2014 at 11:11 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
> On Sat, Dec 13, 2014 at 8:58 PM, Junhwan Choi (최준환) <choi.junhwan at gmail.com>
> wrote:
>>
>> Thank you Nathan,
>>
>> I change Density to density and still experience the errors.
>> I paste the error message on https://bpaste.net/show/bfff704acb9c
>> However, I would like to see some basic documents regarding this
>> issue, if there is any new tip for particle data dealing in yt.
>> For example, I would like to know how to make dark matter density
>> field and something more.
>
>
> Hmm, I've never seen an error like this actually.  This looks like a yt bug.
> All I can say based on the traceback is that this is happening at a low
> level right after we read the data off disk.
>
> Is there any chance you can share the dataset you're trying to load?  Your
> dataset might be breaking an assumption we're making somewhere in the gadget
> frontend. We've had a lot of success sharing big datasets on the mailing
> list using Google drive or dropbox.
>
I will share the data with you through the dropbox.
I will send invitation to you soon after I upload the data into dropbox.

> You can visualize the dark matter density (and most other particle fields)
> using the deposition functionality.  Deposit fields are a special type of
> field that yt computes by depositing particle quantities onto a mesh -
> specifically an octree mesh for Gadget data.
>
> There's some documentation for deposit fields in the field documentation
> here:
>
> http://yt-project.org/docs/dev/analyzing/fields.html
>
> You can see a fully worked out example of how to use a deposition field in
> this notebook:
>
> http://yt-project.org/docs/dev/examining/generic_particle_data.html?highlight=generic%20particle%20data
>
> There's also this notebook specifically about gadget data:
>
> http://yt-project.org/docs/dev/cookbook/gadget_notebook.html?highlight=gadget
>
Thank you, I will read these documents.

Junhwan
>>
>>
>> Thank you,
>> Junhwan
>>
>> On Sat, Dec 13, 2014 at 10:51 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>> >
>> >
>> > On Sat, Dec 13, 2014 at 8:48 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> > wrote:
>> >>
>> >>
>> >>
>> >> On Sat, Dec 13, 2014 at 8:46 PM, Junhwan Choi (최준환)
>> >> <choi.junhwan at gmail.com> wrote:
>> >>>
>> >>> Hi yt users and developers:
>> >>>
>> >>> I try to use yt to visualize my gadget output (hdf5 format).
>> >>> I made following simple script:
>> >>> ========================
>> >>> import matplotlib as matplotlib
>> >>> matplotlib.use('Agg')
>> >>> import matplotlib.pylab as pylab
>> >>> import yt
>> >>>
>> >>> ds = yt.load("snap_agora_100.hdf5")
>> >>>
>> >>> print ds.field_list
>> >>> print ds.derived_field_list
>> >>>
>> >>> pc = yt.ProjectionPlot(ds, "x", ('gas', 'Density'))
>> >>
>> >>
>> >> I think it will work if you use ('gas', 'density')
>> >>
>> >> (note the lower-case D)
>> >>
>> >> If that doesn't work, can you pastebin the error you're seeing, along
>> >> with
>> >> the traceback?  We have paste.yt-project.org for this purpose.
>> >
>> >
>> > Which is unfortunately down at the moment - bpaste.net or
>> > gist.github.com
>> > are good alternatives.
>> >
>> >>
>> >>
>> >>>
>> >>> pc.save("gadget")
>> >>> ==========================
>> >>> But it results in unknown error messages.
>> >>> And, I have searched some documents for yt for gadget, but there is
>> >>> also nothing I can find.
>> >>> Is there any yt gadget documents I can consult ?
>> >>> I have used yt for my enzo simulation analysis.
>> >>>
>> >>> Thanks in advance,
>> >>> Junhwan Choi
>> >>> _______________________________________________
>> >>> yt-users mailing list
>> >>> yt-users at lists.spacepope.org
>> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> >
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