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

[Britton Smith]

Hi Dan,

I did indeed write the frontend for Gadget FOF catalogs and I would be glad
to help you get your data loaded in.

For Gadget FOF datasets, all of the cosmological parameters are stored as
hdf5 attributes in a group called Header.  In the bit of code you posted,
hvals is a dictionary containing all of the hdf5 attributes read in from
the Header group.  It's possible that the name of the attribute storing
omega_lambda has simply been changed from OmegaLambda to something else.
Variable name changes have been known to happen in the Gadget codebase, so
it's definitely possible.

If this is all it is, then what we should do is alter this frontend to try
a few different names to get the various cosmological parameters.  That
should be quite easy to do and I could show you where to make the necessary
changes and you could issue a pull request.  If there are further
differences, it may be best to create a new frontend specifically for this
data type.  I can't imagine there would be huge differences in the data
format, so this shouldn't be too hard either.  If you were able to provide
me with a sample dataset to test against, I would be happy to look at this.

Britton

On Mon, Feb 22, 2016 at 3:23 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> 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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>
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