Eric and Sam,
Yeah. that makes sense. It boils down to the resolution of the box.
A question to Sam ... How did you get "mass resolution is about 2e10M_solar" ?
I am getting 5e9M_solar as the mass of each dark matter particle. And the number of particles in a 1e13M_solar halo is 2000.
ID mass particles density x y z centreofmass x centerofmass y centerofmass z
3700 9.853250284e+12 2000 1.136880784e+04 3.619545698e-01 4.593685567e-01 8.036487699e-01 3.618929449e-01 4.593253520e-01 8.041266519e-01
So I guess for 250 particles, I can try...
virial_filters=[['TotalMassMsun','>=','1.25e12']]
A question to Eric :
Actually, I don't care for the resolution of the halos. I am analyzing the suppression of matter power spectrum as a function of neutrino mass. Which means I am interested only on the semi-linear scales of 20-60 Mpc/h. Towards this, I wish to extract small galaxy groups (upto 1e13M_solar) from my simulation. So, can I regard the HaloFinder halos as blobs, w/o caring for the resolution ? If yes, can I include halofinder halos with as low as 50-100 particles (since they are still halos, regardless of the resolution) ?
I will appreciate if I can get some opinion on this.
shankar
-----Original Message-----
From:
yt-users-bounces@lists.spacepope.org on behalf of Eric Hallman
Sent: Tue 12/8/2009 4:53 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] r_min in HaloProfiler
Shankar,
sam is right on the money with his analysis. Although the halo
finders identify a large number of halos in your simulation they are
very poorly resolved, and so this filter will rule them out on the
basis of not getting to OD of 200. Our analysis with enzo shows that
you can not expect the halos to be resolved under a few hundred
particles as sam suggests.
I would take a look at how many halos are above 500 particles or so
and only run your analysis on those. I suspect it is possible that
one of the reasons you are not seeing speedup with the parallel runs
is that you don't have enough work for the processors given the small
number of virialized halos that you'll actually analyze with this
filter.
On Dec 8, 2009, at 3:30 PM, Sam Skillman wrote:
Shankar,
In a box size of 200 Mpc/h^3 and 512^3 particles, your mass
resolution is about 2e10M_solar. That means in a 10^13 M_solar
halo, you have at most ~500 particles in your halos, which is well
resolved. The main problem with what you're doing is putting an
upper limit on the mass of the halos that you are profiling, which
is opposite to what one normally does. Even if you want to be
cavalier with what you call a halo, you definitely don't want to go
much below 2-5e12 since then you're talking 100 particles. I
personally don't trust profiles unless they have a few thousand
particles, because then I might believe the hydro is resolved. My
guess is that if you do:
virial_filters=[['TotalMassMsun','>=','5e12']]
you'll have more luck with them actually being virialized.
Main point:
If you want to study halos with masses less than 10^13, you're using
the wrong simulation (i.e. too large of a physical box size or too
small of a grid).
Sam
On Tue, Dec 8, 2009 at 3:04 PM, Agarwal, Shankar <sagarwal@ku.edu>
wrote:
Sam,
I am trying to get the virial masses of the halos (with mass upto 1e
+13 Msun) with this filter...
hp.add_halo_filter(HP.VirialFilter, must_be_virialized=True,
overdensity_field='ActualOverdensity',
virial_overdensity=200,
virial_filters=[['TotalMassMsun','<=','1e13']],
virial_quantities=['TotalMassMsun','RadiusMpc'])
But when I look at the radial_profiles/Halo_xxxx_profile.dat files,
I see that none of the halos are virialized. The peak halo densities
are reaching about 20*mean_matter_density. I began my 200Mpc/h Box
with 512^3 particles simulation at z=99. I have not looked at the
literature in great detail but is there something fishy here ?
shankar
-----Original Message-----
From: yt-users-bounces@lists.spacepope.org on behalf of Sam Skillman
Sent: Tue 12/8/2009 3:23 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] r_min in HaloProfiler
Shankar,
r_min is defined in your email:
r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc']
it's twice the smallest dx in units of mpc, dx being the smallest
cell size.
it is being rejected because your halo has something like 3 cells
(radial)
in it, which is almost certainly not resolved.
sam
On Tue, Dec 8, 2009 at 2:11 PM, Agarwal, Shankar <sagarwal@ku.edu>
wrote:
Hi,
While running HaloProfiler, I am seeing this...
P001 yt.lagos ERROR 2009-12-08 15:53:22,403 Skipping halo
with r_max
/ r_min = 1.885682.
I looked at yt/extensions/HaloProfiler.py...
r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc']
if (halo['r_max'] / r_min < PROFILE_RADIUS_THRESHOLD):
mylog.error("Skipping halo with r_max / r_min =
%f." %
(halo['r_max']/r_min))
r_max would be the distance to the furthest particle in the halo
as found
by HaloFinder.
But what is r_min ? And what is the basis for skipping this halo ?
shankar
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Samuel W. Skillman
DOE Computational Science Graduate Fellow
Center for Astrophysics and Space Astronomy
University of Colorado at Boulder
samuel.skillman[at]colorado.edu
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University of Colorado at Boulder
samuel.skillman[at]colorado.edu
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