[yt-users] HaloProfiler ActualOverdensity
Agarwal, Shankar
sagarwal at ku.edu
Wed Dec 2 14:40:13 PST 2009
Britton and Eric,
So I guess if the convention in halo_profiler is (Baryon + Dark Matter Density) / (Mean density) , then I should use
virial_overdensity = 200/Omega_matter = 200/0.258 = 775
instead of 200.
A separate stupid question :
I have run a Box=200Mpc/h with 512^3 dark matter particle simulation. http://drop.io/slice
The most dense point in the box is only 1.3e-27 gm/cm^3, which is about 520*matter_mean_density (for omega_matter=0.26).
Then I ran halo_profiler.py on it. Here are the first few lines...
ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight
1.411083e+03 1.884580e+73 5.022445e-28 1.086579e+00 3.470612e+07 3.350352e+13 4.667973e+12
1.349560e+03 2.826870e+73 2.846061e-28 1.108807e+00 2.697442e+07 4.806416e+13 1.054647e+12
1.199229e+03 3.298015e+73 3.425752e-28 1.131491e+00 2.577368e+07 4.982850e+13 8.115086e+11
1.029234e+03 5.653740e+73 2.792583e-28 1.154639e+00 3.303925e+07 7.331169e+13 2.847611e+12
1.135776e+03 7.538320e+73 3.070320e-28 1.178260e+00 3.784802e+07 1.078674e+14 2.675091e+12
1.135776e+03 7.538320e+73 nan 1.202365e+00 nan 1.078674e+14 0.000000e+00
1.135776e+03 7.538320e+73 nan 1.226962e+00 nan 1.078674e+14 0.000000e+00
1.018853e+03 8.951755e+73 3.040255e-28 1.252063e+00 3.025227e+07 1.149060e+14 1.974464e+12
9.159449e+02 1.083633e+74 1.950294e-28 1.277677e+00 3.573580e+07 1.250475e+14 1.774217e+12
9.158806e+02 1.177862e+74 1.275998e-28 1.303816e+00 3.568055e+07 1.359117e+14 5.672694e+11
8.432311e+02 1.413435e+74 1.915018e-28 1.330489e+00 2.360579e+07 1.501570e+14 1.880053e+12
7.995894e+02 1.649007e+74 2.735319e-28 1.357708e+00 2.651133e+07 1.661165e+14 2.674878e+12
Looking at ActualOverdensity column, Is it possible to have a halo with overdensities in 1000's when the peak overdensity is 520.
And do the "nan" correspond to some kind of profile maxima ?
regards
shankar
-----Original Message-----
From: yt-users-bounces at lists.spacepope.org on behalf of Eric Hallman
Sent: Wed 12/2/2009 12:56 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] HaloProfiler ActualOverdensity
Shankar and Britton,
I have gone through this argument extensively, and discovered that
both definitions are used, with roughly equal frequency in the
literature. Lately, it has been trending toward OD = density/mean
density (matter). I think the main reason for the density with respect
to critical in the past has been due to an historical preference for
omega_m=1 universes (SCDM).
cheers,
On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:
> Shankar,
>
> As I stated in my previous email, you will find both definitions
> used in the literature. I'm not going to spend time in a citation
> battle. The good news is that both definitions differ only by a
> factor of Omega_matter, so you can change the value of
> virial_overdensity accordingly.
>
> Britton
>
> On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
> Hi Britton,
>
> I just wanted a clarification on the definition of
> ActualOverdensity. In your mail, you said...
>
> "ActualOverdensity has the same physical meaning as the regular
> Overdensity
> field. It is (Baryon Density + Dark Matter Density) / (Mean
> density of the
> universe). If you search the literature, you will find alternate
> definitions that use critical density instead of mean density. The
> one used
> here is a little more common."
>
>
> Are you sure you did not mean (Baryon Density + Dark Matter
> Density) / (critical density) ?
>
>
> Because, in halo_profiler.py, there is a virial filter...
>
> hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True,
> overdensity_field='ActualOverdensity',
> virial_overdensity=200,
> virial_filters=[['TotalMassMsun','>=','1e14']],
> virial_quantities=['TotalMassMsun','RadiusMpc'])
>
>
> Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
>
>
> shankar
>
>
>
>
> -----Original Message-----
> From: yt-users-bounces at lists.spacepope.org on behalf of Britton Smith
> Sent: Wed 11/25/2009 1:30 PM
> To: Discussion of the yt analysis package
> Subject: Re: [yt-users] Hop vs HaloProfiler
>
> Hi Shankar,
>
> I will answer the HaloProfiler related questions and leave the Hop
> questions
> for Stephen. However, could you post the failure output for what
> you tried
> to do with Hop. That will probably be helpful for answering your
> question.
>
> Is Halo_0000_profile.dat related to the first Halo listed in
> HopAnalysis.out
> > file ?
> >
>
> Yes, the HaloProfiler will always use the same indices for halos as
> all of
> the halo finders in yt. So, the file Halo_N_profile.dat will always
> refer
> to halo N on the halo list.
>
> What is # ?
> >
>
> This is just a comment character so that plotting programs don't try
> to read
> in what's on that line. The tab between it and the first field name
> is
> there to accommodate the routines that read those files back in to the
> HaloProfiler.
>
>
> > What is the meaning of ActualOverdensity ? And units ?
> >
>
> ActualOverdensity has the same physical meaning as the regular
> Overdensity
> field. It is (Baryon Density + Dark Matter Density) / (Mean density
> of the
> universe). If you search the literature, you will find alternate
> definitions that use critical density instead of mean density. The
> one used
> here is a little more common (I think, but I'm not sure). As per
> these
> definitions, overdensity is a unitless quantity.
>
> In yt, there is an Overdensity field that is calculated on a cell-by-
> cell
> basis. For calculation of virial quantities for halos, the
> overdensity you
> calculate should be explicitly the total mass (baryon + dm) / total
> volume /
> mean density, where total refers to all cells enclosed within the
> sphere of
> the radial profile, not just the shell from r_(i-1) to r_i.
> Technically,
> you could get this by doing a profile of the Overdensity field,
> weighted by
> CellVolume, with accumulation set to True. However, if for some
> reason, the
> user wanted to do profiles of the overdensity field in a different
> way, say
> weighted by CellMass, or just counting the material shell-by-shell
> (accumulation=False), this number would not be correct for the
> calculation
> of virial quantities. For that reason, the HaloProfiler automatically
> generates this ActualOverdensity field which is assured to be
> calculated in
> the correct way. That way the user doesn't accidentally override a
> proper
> calculation of the overdensity used for the virial quantities.
>
> Other than the ActualOverdensity field (which is automatically
> generated by
> the HaloProfiler, and thus does not exist outside that context) you
> can
> always get the units of any field with:
> lagos.fieldInfo[some_field].units
> For more information, see here:
> http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-are
>
> What is the meaning of CellVolume? And units ?
>
> What is Density referring to ? And units ?
> >
> CellVolume and Density are the volume of a cell and the baryon
> density. In
> this context, they are the values of those fields in the radial
> profile. If
> you did it as per the recipe, the CellVolume is the total
> accumulated volume
> for all cells within the sphere radius. Density SHOULD be the
> mass-weighted, mean baryon density for cells within spherical shells.
> However, after looking at the recipe on the website, I see that, in
> error, I
> set the weight_field of the Density profile to None, instead of
> CellMassMsun. Therefore, the Density profile may be meaningless as
> is. I
> will change the recipe on the website ASAP.
>
>
> > What is mywieght ?
> >
>
> The myweight field is a temporary field for keeping track of the
> weight
> field for a weight radial profile. It should be ignored and we
> might just
> want to not write it out in the future.
>
>
> > I also got the projection/ directory. But I got errors...
> >
>
> It looks like the HaloProfiler tried to do a projection of
> Metallicity, but
> your simulation data did not have the MetalDensity field. You need
> to set
> CosmologyUseMetallicityField (or something like that) to 1 in your
> enzo
> parameter file in order to get this field. You can also just remove
> the
> line in the HaloProfiler recipe that adds the metallicity field to
> the list
> of projections.
>
> Cheers,
>
> Britton
>
>
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Dr. Eric J. Hallman
NSF Astronomy and Astrophysics Postdoctoral Fellow
Center for Astrophysics and Space Astronomy
University of Colorado at Boulder
hallman (at) casa.colorado.edu
Phone: (312) 725-4626
http://solo.colorado.edu/~hallman/
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