[yt-users] r_min in HaloProfiler

Sam Skillman samskillman at gmail.com
Tue Dec 8 20:19:55 PST 2009 

Shankar,

Looks like I must have screwed up by a factor of four in my calculation
earlier.  So yeah, 1.25e12 should give you ~250 particles. Whether or not
those objects are converged is another question, and something you'll have
to investigate.

Sam

On Tue, Dec 8, 2009 at 7:25 PM, Agarwal, Shankar <sagarwal at ku.edu> wrote:

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