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

[John Wise]

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
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-- 
John Wise
Assistant Professor of Physics
Center for Relativistic Astrophysics, Georgia Tech
http://cosmo.gatech.edu
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