For question 1, you would use that only if you believe the *correct* OD for virialization is 200 only with respect to either mean matter density or critical density.  The number 200 is somewhat arbitrary.  But for your purposes, your conversion is correct.  As to which number you should use for virial overdensity, I would recommend looking through linear collapse theory in an expanding universe if you are concerned at this level which is correct (e.g. Peebles or the Press-Schechter papers, or any of the new ones)

On Dec 2, 2009, at 3:40 PM, Agarwal, Shankar wrote:

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

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@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@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...

overdensity_field='ActualOverdensity',
virial_overdensity=200,
virial_filters=[['TotalMassMsun','>=','1e14']],

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@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
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
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
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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