[yt-users] Field extraction from arbitrary grids

[Matthew Turk]

Hi Carla,

It's possible that it's writing out the particle values.  If you
explicitly ask for ["gas", "temperature"] it may write that value out.
You can control how the values are deposited on the grid by specifying
smoothed, deposited, etc fields.

On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt
<carla.j.bernhardt at gmail.com> wrote:
> 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 at 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 at 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 at 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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>>> >
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>>
>>
>
>
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