On Fri, Nov 6, 2015 at 9:14 AM, Max Gronke <max.gronke@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@gmail.com> wrote:
>
>
> On Thursday, November 5, 2015, Max Gronke <max.gronke@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@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@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@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@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@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@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@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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