[yt-users] Field extraction from arbitrary grids

[Carla Bernhardt]

Hi Matthew,

Thank you for the suggestion. That works much better for the temperature
field. I also need, however, HI_Density and HII_Density and these do not
seem to be within the "gas" (here is the Traceback
<https://pastebin.com/CKHsXDd5> from when I try that). This is the field
list <https://pastebin.com/44ZtK8JU> from my data, do you have any
suggestions for how I could also extract the HI_Density and HII_Density
successfully?

Thanks,
Carla

2017-07-20 16:38 GMT+02:00 Matthew Turk <matthewturk at gmail.com>:

> 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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