[yt-users] Problem with smoothed covering grid

Nathan Goldbaum nathan12343 at gmail.com
Fri Nov 6 07:24:16 PST 2015


On Fri, Nov 6, 2015 at 9:14 AM, Max Gronke <max.gronke at astro.uio.no> wrote:

> Hi Nathan!
>
> Thanks for the reply. This is a MWE to my problem:
> http://paste.yt-project.org/show/6027/


OK, I'll try to take a look at this.


>
>
> About the error I was getting when I tried to use Bili Dong's feature
> for convenience (as far as I can see it does the same to create a
> volume weighted field as I do): Probably this was because I was doing
> a mistake in checking out the other yt head (f264885 instead of
> 9f560b7).
>

Yup, you want to be on the head with the "development" bookmark (To update
to it and deactivate the bookmark, do: "hg update development" then "hg
bookmark -i development")

-Nathan


>
> Best,
> Max
>
>
> On 6 November 2015 at 14:34, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> >
> >
> > On Thursday, November 5, 2015, Max Gronke <max.gronke at astro.uio.no>
> wrote:
> >>
> >> Hi Nathan & all!
> >>
> >> Sorry for digging up this old topic again (wasn't sure if I should
> >> open another thread or this is fine).
> >> Although I didn't manage to compile the head of yt where Bili Dong's
> >> pull request is included properly, I succeeded in adding a
> >> volume_weighted_smoothed_field as he did.
> >>
> >>
> >>
> >
> > Can you share the compilation error you ran into? It's a big problem if
> > people are unable to compile the latest development version of yt.
> >
> >>
> >>  (with
> >> > fn_smooth =
> >> > add_volume_weighted_smoothed_field("all","particle_position",
> >> > "particle_mass", "smoothing_length",
> >> >                                                "particle_density",
> >> > "particle_density", ds.field_info, 64)[0]
> >> )
> >> Afterwards I can also access the data through
> >> > ad = ds.all_data()
> >> > ad[fn_smooth]
> >>
> >> but I cannot create a covering grid using the newly created field:
> >> > ds.covering_grid(level, left_edge=ds.domain_left_edge, dims = dims,
> >> >                            fields=[fn_smooth])
> >> fails with the error message
> >> > YTFieldNotFound: Could not find field '('deposit',
> >> > 'all_smoothed_particle_density')' in ParticleData.
> >>
> >> The reason seems to be that `fn_smooth` is in "ds.field_info" but not
> >> in " ds.derived_field_list".
> >>
> >> Maybe the my whole ansatz is also wrong? All I want to achieve is to
> >> obtain a covering grid which used the SPH kernels of the particles and
> >> I follow roughly your code in the "Gadget" frontend.
> >
> >
> > Can you create a test script that produces your error? That way one of us
> > can read run the script locally and try to debug. If you can make the
> test
> > script use of one of the test Gadget datasets on yt-project.org/data,
> that
> > would also make it easier for one of us to reproduce your error.
> >
> > You can use paste.yt-project.org to share your full compilation error
> and
> > test script without needing to paste them into an e-mail.
> >
> > Best
> >
> > Nathan
> >
> >>
> >>
> >> Thanks again for your help,
> >> Max
> >>
> >>
> >> On 6 October 2015 at 17:29, Max Grönke <maxbg at astro.uio.no> wrote:
> >> > Thanks!
> >> >
> >> > For the moment we found a workaround (generic sph --> gadget) but for
> >> > the future this might come handy.
> >> >
> >> > Best,
> >> > Max
> >> >
> >> > On 6 October 2015 at 17:14, Nathan Goldbaum <nathan12343 at gmail.com>
> >> > wrote:
> >> >> Hi Max,
> >> >>
> >> >> This actually related to a new feature Bili Dong recently added:
> >> >>
> >> >>
> >> >>
> https://bitbucket.org/yt_analysis/yt/pull-requests/1769/add-add_smoothed_particle_field/diff
> >> >>
> >> >> This PR adds new functionality to make it easier to define SPH
> smoothed
> >> >> fields. Maybe that will help?
> >> >>
> >> >> -Nathan
> >> >>
> >> >> On Tue, Oct 6, 2015 at 1:48 AM, Max Grönke <max.gronke at astro.uio.no>
> >> >> wrote:
> >> >>>
> >> >>> Hi Nathan.
> >> >>> Thanks for your reply. Here's the new link:
> >> >>> http://paste.yt-project.org/show/5930/
> >> >>>
> >> >>> I think I figured out the problem -- at least in theory ;)  I guess
> >> >>> what I need is a "smoothed field". This meant I played around with
> >> >>> "add_volume_weighted_smoothed_field". But although
> >> >>>
> >> >>> > fn_smooth =
> >> >>> > add_volume_weighted_smoothed_field("all","particle_position",
> >> >>> > "particle_mass", "smoothing_length",
> >> >>> >                                               "particle_density",
> >> >>> > "particle_density", ds.field_info, 64)
> >> >>>
> >> >>> (where `ds' is my YT Particle Data Set)
> >> >>>
> >> >>> seems to work, I cannot access the newly created field?
> >> >>> ("YTFieldNotFound: Could not find field '('deposit',
> >> >>> 'all_smoothed_particle_density')' in ParticleData.")
> >> >>>
> >> >>> Thanks for your help,
> >> >>> Max
> >> >>>
> >> >>>
> >> >>> On 5 October 2015 at 17:41, Nathan Goldbaum <nathan12343 at gmail.com>
> >> >>> wrote:
> >> >>> > Hi Max,
> >> >>> >
> >> >>> > I'm unable to load the pastebin link in your e-mail.  Can you
> >> >>> > re-send
> >> >>> > using
> >> >>> > a different pastebin service? We have paste.yt-project.org set up
> >> >>> > for
> >> >>> > this
> >> >>> > purpose.
> >> >>> >
> >> >>> > Matt also has an open pull request that among other things adds
> >> >>> > support
> >> >>> > to
> >> >>> > arbitrary_grid for fluid fields:
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> >
> https://bitbucket.org/yt_analysis/yt/pull-requests/1763/numpy-like-operations/diff
> >> >>> >
> >> >>> > -Nathan
> >> >>> >
> >> >>> > On Fri, Oct 2, 2015 at 10:23 AM, Max Grönke
> >> >>> > <max.gronke at astro.uio.no>
> >> >>> > wrote:
> >> >>> >>
> >> >>> >> Hi Matthew,
> >> >>> >>
> >> >>> >> thanks for your prompt response!
> >> >>> >>
> >> >>> >> I tried the covering_grid first but as I said we had problems
> with
> >> >>> >> a
> >> >>> >> lot of zero-valued grid points. It seems the values from the
> >> >>> >> coarser
> >> >>> >> grid are not duplicated downwards?
> >> >>> >> I tried to post a MWE to illustrate what I mean:
> >> >>> >> http://pastebin.com/yishxbjW
> >> >>> >>
> >> >>> >> For the arbitrary_grid: It says it cannot deal with fluid
> >> >>> >> variables?
> >> >>> >>
> >> >>> >> Best,
> >> >>> >> Max
> >> >>> >>
> >> >>> >> On 2 October 2015 at 16:44, Matthew Turk <matthewturk at gmail.com>
> >> >>> >> wrote:
> >> >>> >> > Hi Max,
> >> >>> >> >
> >> >>> >> > Ah, I think I see the problem.  If you're doing any type of
> >> >>> >> > particle
> >> >>> >> > deposition, including smoothing, you might be better suited to
> >> >>> >> > using
> >> >>> >> > the arbitrary_grid or the covering_grid objects, as
> >> >>> >> > smoothed_covering_grid is designed for situations where values
> >> >>> >> > need
> >> >>> >> > to
> >> >>> >> > be interpolated through a cascade of refinements.  It'd
> probably
> >> >>> >> > end
> >> >>> >> > up being faster to use either arbitrary_grid or covering_grid,
> >> >>> >> > too.
> >> >>> >> > Can you try that and let us know if it meets your needs?
> >> >>> >> >
> >> >>> >> > -Matt
> >> >>> >> >
> >> >>> >> > On Fri, Oct 2, 2015 at 9:42 AM, Max Grönke
> >> >>> >> > <max.gronke at astro.uio.no>
> >> >>> >> > wrote:
> >> >>> >> >> Hi everybody!
> >> >>> >> >>
> >> >>> >> >> I followed loosely the example provided here
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >>
> http://yt-project.org/docs/dev/examining/low_level_inspection.html#examining-grid-data-in-a-fixed-resolution-array
> >> >>> >> >> but encountered an error message using a smoothed covering
> grid
> >> >>> >> >> with
> >> >>> >> >> SPH data instead of a covering grid. I posted an MWE here:
> >> >>> >> >> http://pastebin.com/2sStpLmw which leads to the error message
> >> >>> >> >> "AttributeError: 'YTSmoothedCoveringGrid' object has no
> >> >>> >> >> attribute
> >> >>> >> >> '_pdata_source' "
> >> >>> >> >>
> >> >>> >> >> I wanted to use a smoothed covering grid because I found that
> >> >>> >> >> using
> >> >>> >> >> SPH data a lot of "holes" are in `covering grid' (but not,
> e.g.,
> >> >>> >> >> in
> >> >>> >> >> a
> >> >>> >> >> slice plot). So I assumed there is some problem in duplicating
> >> >>> >> >> the
> >> >>> >> >> values from the coarser grids?
> >> >>> >> >>
> >> >>> >> >> My yt version is 3.2-dev.
> >> >>> >> >>
> >> >>> >> >> Thanks a lot for your time & help,
> >> >>> >> >> Max
> >> >>> >> >> _______________________________________________
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> >> >>> >> >>
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