[yt-users] Problem with smoothed covering grid

Max Gronke max.gronke at astro.uio.no
Fri Nov 6 02:43:33 PST 2015 

Hi Matthew.
Same error:
> YTFieldNotFound: Could not find field '('deposit', 'all_smoothed_particle_density')' in ParticleData.

Best,
Max


On 5 November 2015 at 15:44, Matthew Turk <matthewturk at gmail.com> wrote:
> 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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