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

[Matthew Turk]

Hi Brian,

On Mon, Jun 15, 2015 at 7:18 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>
>> 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.
>

I'm hesitating to push us further into the weeds here when you've
given a very thoughtful and helpful reply to Junhwan, but
arbitrary_grid can be flat along one dimension (i.e., NxMx1) and was
designed for this use case.

-Matt

> --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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