[yt-users] r_min in HaloProfiler

Agarwal, Shankar sagarwal at ku.edu
Tue Dec 8 18:25:29 PST 2009


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 at 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 at 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 at 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 at 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 at 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
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
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Eric Hallman
Google Voice: (312) 725-HMAN
hallman13 at gmail.com




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