[yt-users] Problem with smoothed covering grid

Max Gronke max.gronke at astro.uio.no
Fri Nov 6 07:14:20 PST 2015


Hi Nathan!

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

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).

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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