Hi Brian, On Mon, Jun 15, 2015 at 7:18 PM, Brian O'Shea <bwoshea@gmail.com> wrote:
yt's "arbitrary_grid" feature might also be useful here.
http://yt-project.org/docs/dev/analyzing/objects.html?highlight=arbitrary_gr...
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@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@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@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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