[yt-users] loading Gadget outputs

Molly Peeples molly at stsci.edu
Wed Jul 27 11:11:10 PDT 2016


Hey Desika, Nathan,

Thanks! That was more painless than I expected :-)

Here’s a celebration image:
[cid:95DEA218-4B08-4334-ACB3-3D3AB7656F01]

—Molly



On July 27, 2016 at 2:00:13 PM, Nathan Goldbaum (nathan12343 at gmail.com<mailto:nathan12343 at gmail.com>) wrote:


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