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.


On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <> 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, there is a virial filter...


Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look


-----Original Message-----
From: 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

> 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:
For more information, see here:

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.



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