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
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>



--
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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--
Samuel W. Skillman
DOE Computational Science Graduate Fellow
Center for Astrophysics and Space Astronomy
University of Colorado at Boulder
samuel.skillman[at]colorado.edu