[yt-users] yt basic visualization for gadget output
Nathan Goldbaum
nathan12343 at gmail.com
Sun Dec 14 15:45:17 PST 2014
When I run "h5ls -r" on the snapshot you shared with me off-list, I get the
following:
goldbaum at ROUS in ~/Dropbox/Gadget_yt_test
○ h5ls -r snap_agora_100.hdf5
/ Group
/Header Group
/PartType0 Group
/PartType0/ArtificialViscosity Dataset {2277264}
/PartType0/Coordinates Dataset {2277264, 3}
/PartType0/Density Dataset {2277264, 2}
/PartType0/ElectronAbundance Dataset {2277264, 2}
/PartType0/H2I Dataset {2277264, 2}
/PartType0/H2II Dataset {2277264, 2}
/PartType0/HI Dataset {2277264, 2}
/PartType0/HII Dataset {2277264, 2}
/PartType0/HM Dataset {2277264, 2}
/PartType0/HeI Dataset {2277264, 2}
/PartType0/HeII Dataset {2277264, 2}
/PartType0/HeIII Dataset {2277264, 2}
/PartType0/InternalEnergy Dataset {2277264, 2}
/PartType0/NeutralHydrogenAbundance Dataset {2277264, 2}
/PartType0/ParticleIDs Dataset {2277264, 2}
/PartType0/Potential Dataset {2277264}
/PartType0/SmoothingLength Dataset {2277264, 2}
/PartType0/Velocities Dataset {2277264, 3}
/PartType1 Group
/PartType1/Coordinates Dataset {2277264, 3}
/PartType1/ParticleIDs Dataset {2277264, 2}
/PartType1/Potential Dataset {2277264}
/PartType1/Velocities Dataset {2277264, 3}
/PartType5 Group
/PartType5/Coordinates Dataset {3206474, 3}
/PartType5/Masses Dataset {3206474, 2}
/PartType5/ParticleIDs Dataset {3206474, 2}
/PartType5/Potential Dataset {3206474}
/PartType5/Velocities Dataset {3206474, 3}
It seems that many of the datasets are matrices with two rows rather than
vectors. Do you know where this is coming from? I don't think I've seen a
gadget hdf5 dataset with this structure before.
Is the data duplicated or has it just been arbitrarily split over two rows,
which we should concatenate internally?
On Sun, Dec 14, 2014 at 4:34 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>
> 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.
>
> Junhwan, what's happening is that your density field on disk is a
> vector, with two elements. (Checking this with h5dump -r on one of
> your hdf5 files should verify that.) If that's intentional, we'll
> need to come up with a way to break the uncertainty as to which one is
> the "right" one. Could you send a link to a paste of h5dump -r on
> your output file? The yt pastebin is back up.
>
> >
> > 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
> >> >>> _______________________________________________
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> >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >
> >> >
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