[yt-users] Dealing with HOP groups

[Sam Skillman]

Since this isn't yt related question anymore, let's move this to a private
conversation.

Sam

On Sun, Feb 28, 2010 at 1:45 PM, Agarwal, Shankar <sagarwal at ku.edu> wrote:

> 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
> >
> >
> > _______________________________________________
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> > 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
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