[yt-users] Problem with smoothed covering grid

Matthew Turk matthewturk at gmail.com
Thu Nov 5 06:44:17 PST 2015 

Hi Max,

Can you try doing:

cg = ds.covering_grid(level, left_edge=ds.domain_left_edge, dims=dims)
cg[fn_smooth]



On Thu, Nov 5, 2015 at 5:10 AM, 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. (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.
>
> 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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