[yt-users] Get particle extent for a non-cosmological simulation

Jared Coughlin Jared.W.Coughlin.29 at nd.edu
Mon Dec 11 10:13:56 PST 2017


Great, thanks! I'll take a look at the in-development version. If you
wouldn't mind pointing me to those commits, I can take a look and work on
it over the holidays, perhaps?
-Jared

On Mon, Dec 11, 2017 at 1:03 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hi Jared,
>
> Unfortunately right now for Gadget data you need to know that information
> before you load your data. Try using a very large bounding box.
>
> I've fixed this behavior in an in-development version of yt which has not
> been upstreamed yet. The code will be part of yt 4.0 (due out sometime in
> 2019 at the moment) so in the future this will be easier. In this new
> version if there's no user-specified bounding box, we scan the file and
> find the min and max particle locations and use those to set the bounding
> box.
>
> If you're interested in trying the new version of yt out, you'll need to
> build yt from source using the "sph-viz" branch on my fork of yt on github (
> https://github.com/ngoldbaum/yt). You'll also need to build and install
> cykdtree (https://github.com/cykdtree/cykdtree) which has been added as a
> dependency of yt.
>
> In principle it should be possible to backport this functionality to the
> current version of yt but it will take a bit of work. If you're interested
> in taking that on I can point you to the commits where I implemented the
> new automatic bounding box detection in the in-development version of yt.
>
> Hope that's helpful,
>
> Nathan
>
> On Mon, Dec 11, 2017 at 11:52 AM, Jared Coughlin <
> Jared.W.Coughlin.29 at nd.edu> wrote:
>
>> Hello! I have a gadget snapshot that was generated from a
>> non-cosmological simulation. This causes yt to ignore the box size
>> parameter. However, when I try to make a plot, yt generally fails because
>> ds.domain_left_edge = ds.domain_right_edge = 0.0. This necessitates that I
>> change those parameters manually. My question is: is there a way to get the
>> domain bounds from the file so that I don't have to set these manually
>> every time?
>>
>> I noticed that if I get the box size wrong, yt complains about particle
>> bounds exceeding the domain bounds, and so I looked a little bit at the
>> code to see if I could figure out how yt was getting these numbers and see
>> if I could just do something similar, but I haven't had a whole lot of
>> luck. It seems that in the compute_morton function there's a pos_x.max and
>> min function, but those are passed in _initialize_index as data having been
>> read from an hdf5 file?
>>
>> I'm not super sure I understand what's going on there, but if anyone has
>> any thoughts, I'd greatly appreciate it. I basically just need the max and
>> min particle positions along each of the x, y, and z directions, but trying
>> ad["Coordinates"] fails unless the bounds are properly set to begin with.
>> Thanks!
>>
>> -Jared
>>
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>
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