[yt-users] r_min in HaloProfiler
Michele Trenti
Michele.Trenti at Colorado.EDU
Tue Dec 8 21:07:50 PST 2009
Hi Shankar,
> 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.
I would strongly reccomend to read O'Shea et al. 2005, ApJS, 160, 1. The
halo mass function in Enzo is not correctly reproduced below ~200-300
particles, even if you use AMR. You start missing a significant number of
halos below that threshold. This is because the use of a PM scheme at very
high z (at the beginning of your simulation) suppresses high frequency
modes in the power spectrum. If you need to study the halo mass
function/power spectrum, then I would suggest you to consider an
alternative code. For example, Gadget2 (Springel 2005) can reproduce
correctly the halo mass function down to ~30 particles and might be better
suited to your needs. Like Enzo, it is public.
Cheers,
Michele
Michele Trenti, Ph.D.
Center for Astrophysics and Space Astronomy
University of Colorado
389 UCB Phone: +1 303-492-8490
Boulder, Colorado 80309-0389 Fax: +1 303-492-7178
USA E-mail: michele.trenti at colorado.edu
"It often happens that a player carries out a deep and complicated
calculation, but fails to spot something elementary right at the first
move." -- Chess Grandmaster Alexander Kotov
On Tue, 8 Dec 2009, Agarwal, Shankar 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
>>
>>
>> _______________________________________________
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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
>> 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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