[yt-users] yt basic visualization for gadget output

Nathan Goldbaum nathan12343 at gmail.com
Sat Dec 13 21:11:15 PST 2014


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.

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,
> 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
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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