[yt-users] wired square in enzo DM slice map

[Brian O'Shea]

>
>
> yt's "arbitrary_grid" feature might also be useful here.
>
>
> http://yt-project.org/docs/dev/analyzing/objects.html?highlight=arbitrary_grid#arbitrary-grid
>


I concur, though if the size of the grid or number of particles is large
(as in the simulation I've been working with) this can result in memory
issues.

--Brian




>
>
>> I hope this helps!
>>
>> Regards,
>> Brian
>>
>>
>>
>> On Mon, Jun 15, 2015 at 5:02 PM, Junhwan Choi (최준환) <
>> choi.junhwan at gmail.com> wrote:
>>
>>> Thank you Nathan,
>>>
>>> As I mentioned in my original inquire, if I use other IC generator
>>> such as CICASS, I do not get this wired square.
>>> I found that the MUSIC generates ParticleDisplacements_x/y/z, while
>>> the CICASS generates ParticlePositions for the DM particle position
>>> information.
>>> If this is the intrinsic enzo issue, there could be a subtle flaw for
>>> the enzo's DM N-body calculation if one uses MUSIC output.
>>> If this is a case, I had better report it to enzo user mailing list…
>>>
>>> Best,
>>> Junhwan
>>>
>>>
>>> On Mon, Jun 15, 2015 at 1:20 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>> > If this is a plot of the Enzo "Dark_Matter_Density" field that gets
>>> written
>>> > to Enzo output files, then the artifacts you're seeing are generated by
>>> > Enzo. yt is just plotting whatever is in your output files.
>>> >
>>> > You should be able to see how Enzo generates this field by grepping the
>>> > codebase for "OutputSmoothedDarkMatter" and looking at the relevant
>>> code
>>> > sections. One key thing: I believe Enzo's CIC deposit machinery doesn't
>>> > handle grid boundary conditions properly, so and particles that should
>>> > contribute to the cells that are at a grid boundary will only
>>> contribute if
>>> > they are on one side of the grid boundary. This would lead to the
>>> deficits
>>> > you're seeing. I haven't looked at that code in a while so please
>>> excuse me
>>> > if I'm misremembering here.
>>> >
>>> > Hope that's helpful,
>>> >
>>> > Nathan
>>> >
>>> > On Mon, Jun 15, 2015 at 9:59 AM, Junhwan Choi (최준환) <
>>> choi.junhwan at gmail.com>
>>> > wrote:
>>> >>
>>> >> Hi yt users,
>>> >>
>>> >> I have asked a similar question previously but I did get partial
>>> >> answer so that I ask again.
>>> >> I have made cosmological IC from MUSIC and run with enzo.
>>> >> I made the DM density map with velocity arrow at z=200 which is
>>> >> initial redshift using yt (and attach the figure).
>>> >> It shows the wired square feature.
>>> >> Previously, John wise suggested me to use enzo SPH smoothing to remove
>>> >> this issue and it worked.
>>> >> But, after test a few more run, I have couple more fundamental
>>> >> questions on this issue.
>>> >>
>>> >> 1) Is this wired square effect is real effect in enzo or
>>> visualization in
>>> >> yt?
>>> >>     If this is an intrinsic enzo effect, we can say that DM gravity
>>> >> calculation at high-z some kind of error.
>>> >>     If this is an visualization effect, I found that other enzo
>>> >> simulation using different IC generator does not show this effect (see
>>> >> question 2).
>>> >>     This difference makes me very confused.
>>> >>
>>> >> 2) I tested with other IC generator and I do not see the wired square
>>> >> feature.
>>> >>     I found that other IC generator output real DM position while
>>> >> MUSIC IC generate displacement of DM particle position.
>>> >>     Can it be the origin of issue?
>>> >>
>>> >>
>>> >> I think this inquiry can go to enzo mailing list or MUSIC developer.
>>> >> If it is necessary, I can ask it to other place.
>>> >>
>>> >> Thank you in advance,
>>> >> Junhwan
>>> >>
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>>> >>
>>> >
>>> >
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