[yt-users] working with general hdf5 data from galaxy simulations

[Nathan Goldbaum]

Hi Dan,

This means that yt isn't able to infer cosmological parameters for that
dataset. It looks like you're trying to load a groups file, which is a
subset of the full dataset, and it's being read in by the Gadget FOF
frontend, which handles group datasets like this for the Gadget simulation
code. Arepo and Gadget are supposed to share identical output formats, but
it looks like the groups file you're trying to load is subtly different
from the sorts of Gadget groups files that yt can already natively load.

Looking at the Gadget FOF frontend, there doesn't appear to be a way to set
cosmology parameters by hand. I think the best approach here is probably to
modify the Gadget FOF frontend to handle Arepo data.

Unfortunately I don't know much about the Gadget FOF frontend - Britton
Smith is the author of that frontend and he may be able to chime in here.

-Nathan

On Mon, Feb 22, 2016 at 1:16 AM, D Mick <danomick at gmail.com> wrote:

> Hello all, yt has some of the greatest plotting capabilities, and I
> greatly enjoy working with yt! Recently I have begun to work with hdf5 data
> from a large scale galaxy simulation (illustris) and I was wondering how I
> can work with the data, is there a general munging procedure for getting it
> into the correct yt format? When I try to plot
>
> import yt
>
> ds = yt.load("Groups_hdf5_plt_cnt_0150")
> yt.SlicePlot(ds, 'x', "density", width = (800.0, 'kpc')).save()
> yt.SlicePlot(ds, 'y', "density", width = (800.0, 'kpc')).save()
> yt.SlicePlot(ds, 'z', "density", width = (800.0, 'kpc')).save()
>
> I get the following error:
>
>
> /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/yt/frontends/gadget_fof/data_structures.pyc
> in _parse_parameter_file(self)
>
> *    151*         self.periodicity = (True, True, True)
>
> *    152*         self.current_redshift = hvals["Redshift"]
>
> --> 153         self.omega_lambda = hvals["OmegaLambda"]
>
> *    154*         self.omega_matter = hvals["Omega0"]
>
> *    155*         self.hubble_constant = hvals["HubbleParam"]
>
>
> KeyError: 'OmegaLambda'
>
>
>
>
> I am guessing this is because the field entries do not match up.
>
>
> Any help is much appreciated!
>
>
> Dan
>
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