[yt-users] loading Gadget outputs

Nathan Goldbaum nathan12343 at gmail.com
Wed Jul 27 10:59:48 PDT 2016


On Wed, Jul 27, 2016 at 12:56 PM, Desika Narayanan <
desika.narayanan at gmail.com> wrote:

> Hey Molly,
>
> I'm not sure about why the Projection plots work but not the Slice plot,
> but I can answer at least some of the questions.
>
> When you have gadget/gizmo snapshot split into multiples (i.e.
> snapshot_100.0.hdf5, snapshot_100.1.hdf5), you should be able to just load
> the '0.hdf5' file, and it will load all of the multiples.
>
> n_ref tells you the maximum number of particles can be in a cell before
> the octree stops splitting (so lower number means finer octree splitting).
>
> over_refine_factor > 0 will refine each cell in the octree one extra time
> even after the n_ref threshold is met.  Increasing this to 1 or 2 will make
> much prettier images, at the cost of memory.
>
> -desika
>
>
>
>
> On Wed, Jul 27, 2016 at 12:50 PM, Molly Peeples <molly at stsci.edu> wrote:
>
>> Hi folks,
>>
>> I am trying to read in a Gadget output that’s split into 16 hdf5 files
>> (fwiw, it’s an EAGLE output, and so “should” be similar to the OWLS
>> format). I need to be able to analyze / render the entire output, not just
>> one of the pieces, but I haven’t been able to figure out how to actually
>> load them (akin to how for Enzo yt figures out that there are a lot of cpu
>> outputs in a directory).
>>
>> I have taken a look at
>> http://yt-project.org/doc/cookbook/owls_notebook.html#owls-notebook, but
>> even there in the example, it’s just reading in the one output and ignoring
>> the other 7 in the example tarball. And there I was having trouble tracking
>> down what n_ref and over_refine_factor refer to.
>>
>> Interestingly, if I load just the single hdf5s, I can get ProjectionPlots
>> to work but not SlicePlots (which insist there’s “zero dynamic range” with
>> “Min = Max = 0.00000”.)
>>
>>
Is this a zoom-in simulation? It might be that you're slicing through a
region that has no gas particles.

What happens if you specify the center of the SlicePlot in a region where
you know there are gas particles? Something like:

    v, c = ds.find_max('density')

    slc = SlicePlot(ds, 2, 'density', center=c)

    slc.save()


> FWIW, yt.__version__ gives me 3.3.1. (And major thanks to Nathan for
>> getting *that* installation to go smoothly!!)
>>
>> Suggestions?
>> —Molly
>>
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>>
>
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