[yt-users] weird square feature in dark matter density slice map

[Junhwan Choi (최준환)]

Hi Matt and others,

I make the Dark_Matter_Density field slice map, and I still see the
weird square feature.
Meanwhile, I also make the gas density field slice map using ('gas', 'density')
and I find that it does not see the square feature.
Is there any intrinsic issue for the particle deposition?
[My collaborator made the same figure from the ramses output and it
does not show the square feature in DM slice map.]

Here, I send a link for the slice maps under my web page, because the
each figure is about 1MB and mailing list does not like it.
Dark_Matter_Density
http://www.as.utexas.edu/~jhchoi/data/cen_all_0000_Slice_z_Dark_Matter_Density.png
gas density
http://www.as.utexas.edu/~jhchoi/data/cen_all_0000_Slice_z_density.png

Thank you,
Junhwan

On Thu, May 14, 2015 at 10:18 AM, John Wise <jwise at physics.gatech.edu> wrote:
> Hi Junhwan,
>
> You can still use the Enzo's intrinsic SPH smoothing kernel for the
> Dark_Matter_Density field, which will consider the nearby particles in the
> ghost zones.  This should remove most (if not, all) of these artifacts.
> Then you can perform your analysis.
>
> Thanks,
> John
>
>
> On 05/14/2015 11:15 AM, Matthew Turk wrote:
>>
>> Hi Junhwan,
>>
>> It's "real" for that particular component, in that buffer particles
>> aren't considered.  Enzo should in its dark matter density field,
>> however.
>>
>> -Matt
>>
>> On Thu, May 14, 2015 at 10:14 AM, Junhwan Choi (최준환)
>> <choi.junhwan at gmail.com> wrote:
>>>
>>> Thank you for your advice,
>>>
>>> I would like to confirm whether the weird square feature is only for
>>> visualization effect or also in real cic computed data.
>>> What I plan to do is to compute power spectrum from the cic data set
>>> that I would get using covering_grid object.
>>> If the particle cic in enzo has intrinsic cic issue, I need to wait
>>> for SPH or find other way.
>>>
>>> Thank you,
>>> Junhwan
>>>
>>>
>>> On Thu, May 14, 2015 at 10:00 AM, Matthew Turk <matthewturk at gmail.com>
>>> wrote:
>>>>
>>>> Hi John,
>>>>
>>>> It can't right now do that, but I've got that on my todo list for the
>>>> next week or so.  I haven't yet implemented "smooth" for grid objects.
>>>>
>>>> -Matt
>>>>
>>>> On Thu, May 14, 2015 at 9:52 AM, John Wise <jwise at physics.gatech.edu>
>>>> wrote:
>>>>>
>>>>> Hi Junhwan,
>>>>>
>>>>> This is an artifact from the cloud-in-cell interpolation.
>>>>>
>>>>> To anyone else, can yt smooth the DM density field with an SPH kernel?
>>>>>
>>>>> Another solution is to use Enzo to smooth the DM density internally
>>>>> with the
>>>>> command line option, "-M" with the usual "-d -r" flags for a restart
>>>>> and
>>>>> debug mode.  This will overwrite the Dark_Matter_Density field with one
>>>>> that's smoothed with a standard SPH kernel.  I would perform this
>>>>> operation
>>>>> on a copy of the data just in case the process failed, in which case
>>>>> the
>>>>> dataset will become corrupted.  Then you would plot
>>>>> "dark_matter_density" in
>>>>> yt.
>>>>>
>>>>> Thanks,
>>>>> John
>>>>>
>>>>>
>>>>> On 05/14/2015 10:33 AM, Junhwan Choi (최준환) wrote:
>>>>>>
>>>>>>
>>>>>> Hi yt users,
>>>>>>
>>>>>> I make a simple dark matter slice map from my enzo simulation output
>>>>>> with following script.
>>>>>> ==================
>>>>>> pc = yt.SlicePlot(ds, "z", ('deposit', 'io_cic'), width = (244.0,
>>>>>> 'Mpccm/h'), center=cen_center)
>>>>>> pc.annotate_text((0.7,0.9),'z=%4.2f' % ds.current_redshift,
>>>>>> coord_system='figure', text_args = text_dict)
>>>>>> pc.annotate_velocity(factor=16, scale=None, scale_units=None,
>>>>>> normalize=False)
>>>>>> pc.save("cen_all_0000")
>>>>>> =================
>>>>>>
>>>>>> I see the weird 5x6 square shapes on the plot.
>>>>>> Why this square/cube shape result from and how to remove this?
>>>>>>
>>>>>> Thank you in advance,
>>>>>> Junhwan
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>> --
>>>>> John Wise
>>>>> Assistant Professor of Physics
>>>>> Center for Relativistic Astrophysics, Georgia Tech
>>>>> http://cosmo.gatech.edu
>>>>> _______________________________________________
>>>>> yt-users mailing list
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>>>>
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>
> --
> John Wise
> Assistant Professor of Physics
> Center for Relativistic Astrophysics, Georgia Tech
> http://cosmo.gatech.edu
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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