[yt-users] Dealing with HOP groups

[Agarwal, Shankar]

Hi Sam,

If I choose option 1, I guess I will need a grid of 512*4=2048. That will resolve 200Mpc/2048=97 Kpc

In that case,

MaximumRefinementLevel = 2
CellFlaggingMethod = 2 4
MinimumOverDensityForRefinement = 2.0 4.0


How important is MinimumOverDensityForRefinement ? I can't decide why I should not use 4.0 8.0 to reduce computing time. And how do these two numbers relate to the VirialOverdensity=200?

Is this something that I will have to figure out only by running a simulation? I am hoping somebody already has experience with large box simulations.

Shankar


-----Original Message-----
From: yt-users-bounces at lists.spacepope.org on behalf of Sam Skillman
Sent: Sun 2/28/2010 1:39 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] Dealing with HOP groups
 
Actually yes.  You could check this yourself by examining the last column in
HopAnalysis out.  If max_r < 2*(1/512)=3.9e-3 then yes, it will skip it.  In
one of my simulations, a 5e11 Msun halo has a max_r of 2.64e-03
corresponding to 168 kpc/h.  The halo profiler was not built for profiling
halos with < 2 cells in radius.  In my mind you have at least four options:

1.  Run with AMR to resolve the dark matter potential so that you can use
the halo profiler as built.  Moderate computational cost.  I'm guessing this
was the case for Stephen's simulation where a decent fraction of the halos
in the HopAnalysis were able to be profiled.
2.  Run with a gigantic unigrid such that you can resolve these halos with >
2 (and preferably many) cells.  This is a very computationally expensive
route as you'd need more than a 2048^3 unigrid in a 200 Mpc box.  I do not
recommend this option.
3.  Write a dark matter particle profiler that uses the particle positions
(and not grid cells) to bin up the profile.  Little computational cost but
requires coding on your part.
4.  Run the same size unigrid on a smaller physical volume to capture a
different range of the mass function.

Cheers,
Sam



On Sun, Feb 28, 2010 at 12:07 PM, Agarwal, Shankar <sagarwal at ku.edu> wrote:

> Hi Sam,
>
> Here is how I am using it right now...
>
> hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True,
>              overdensity_field='ActualOverdensity',
>              virial_overdensity=200,
>               virial_filters=[['TotalMassMsun','>=','5e11']],
>              virial_quantities=['TotalMassMsun','RadiusMpc'])
> hp.make_profiles(filename="VirialHaloes.out")
>
> And i get 500.
>
>
> Do you think it has something to do with the grid spacing (for 512 ^3 grid
> in 200 Box, it is 390 Kpc)
>
> HaloProfiler may be skipping small halos completely since they are smaller
> than 390 Kpc.
>
>
> Shankar
>
>
> -----Original Message-----
> From: yt-users-bounces at lists.spacepope.org on behalf of Sam Skillman
> Sent: Sun 2/28/2010 12:34 PM
> To: Discussion of the yt analysis package
> Subject: Re: [yt-users] Dealing with HOP groups
>
> Hi Shankar,
>
> Do you have a line that looks like:
> hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True,
>                   overdensity_field='ActualOverdensity',
>                   virial_overdensity=200,
>                   virial_filters=[['TotalMassMsun','>=','1e14']],
>                   virial_quantities=['TotalMassMsun','RadiusMpc'])
>
> If so, please post it.  The number of halos > 10^14 Msun is fairly close to
> 500 in a 200 Mpc box.  If you want the halo profiler to use all halos, set
> virial_filters=[['TotalMassMsun','>=','1e14']]  accordingly.
>
> Sam
>
> On Sun, Feb 28, 2010 at 11:08 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
>
> > Hi Stephen,
> >
> > I read
> >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2009-March/000110.html
> >
> > Do you remember the cosmology parameters for your run: particles, grid,
> > box, refinement, AMR ON or OFF ?
> >
> >
> > I have run a 200 Mpc/h box, 512^3 particle, 512^3 grid, AMR-OFF
> simulation
> > and I get about 30,000 halos using HOP. When I try to finding virial
> halos,
> > I get only 500. I may have to increase the grid to 1024^3.
> >
> > Let me know how you got 40,000 virial halos.
> >
> > Thanks
> > 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

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