Hi yt-users,

I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:

obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])

and extract the desired fields:

temp = obj["temperature"]
HIdens = obj["HI_Density"]

(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.

Cheers,
Carla

2017-07-12 12:35 GMT+02:00 Carla Bernhardt <carla.j.bernhardt@gmail.com>:
Hi Matthew,

Thank you for your reply. I was using yt Version 3.2.3 and am working out some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.

Cheers,
Carla


2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk@gmail.com>:
Hi Carla,

Interesting.  It's possible, for the call to "temperature" (which
raises NotImplementedError) that the version of yt you're on doesn't
yet support mesh fields in arbitrary grids; that was added reasonably
recently.  For the others, I'm not totally sure why it's breaking --
which version of yt are you using, and what type of data?  It may just
be that they aren't deposit fields.  In that case, try explicitly
stating obj["gas","temperature"] or obj["gas","HI_Density"].  It may
also be that the aliasing is getting in the way, in which case instead
of "HI_Density" you might need to try "Hp0_density".

On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt
<carla.j.bernhardt@gmail.com> wrote:
> Dear yt-users,
>
> I am trying to extract a unigrid data cube within a specific region and
> specified dimensions, thus I am using arbitrary_grid(), however, beyond the
> example given in the docs, my field extractions all fail. I would like to
> extract temperature, HI_Density and HII_Density. Here is a snippet from my
> code:
>
> obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])
> print(obj["deposit", "all_density"])
> print(obj["temperature"])
> print(obj["HI_Density"])
>
> The line print(obj["deposit", "all_density"]) works, but the two lines after
> both fail. Here is the traceback from the temperature, and I even tried out
> deposited temperature and deposited HI_Density. Am I formatting this
> incorrectly, or is there a different way to extract the fields?
>
> Kind regards,
> Carla Bernhardt
> PhD Student
> ZAH Institut für Theoretische Astrophysik
> Universität Heidelberg
>
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> yt-users mailing list
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