Shankar,<br><br>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.<br>
<br>Britton<br><br><div class="gmail_quote">On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <span dir="ltr"><<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Britton,<br>
<br>
I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said...<br>
<br>
"ActualOverdensity has the same physical meaning as the regular Overdensity<br>
field. It is (Baryon Density + Dark Matter Density) / (Mean density of the<br>
universe). If you search the literature, you will find alternate<br>
definitions that use critical density instead of mean density. The one used<br>
here is a little more common."<br>
<br>
<br>
Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ?<br>
<br>
<br>
Because, in halo_profiler.py, there is a virial filter...<br>
<br>
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True,<br>
overdensity_field='ActualOverdensity',<br>
virial_overdensity=200,<br>
virial_filters=[['TotalMassMsun','>=','1e14']],<br>
virial_quantities=['TotalMassMsun','RadiusMpc'])<br>
<br>
<br>
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look <a href="http://arxiv.org/abs/astro-ph/0011495" target="_blank">http://arxiv.org/abs/astro-ph/0011495</a><br>
<br>
<br>
shankar<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:yt-users-bounces@lists.spacepope.org">yt-users-bounces@lists.spacepope.org</a> on behalf of Britton Smith<br>
Sent: Wed 11/25/2009 1:30 PM<br>
To: Discussion of the yt analysis package<br>
Subject: Re: [yt-users] Hop vs HaloProfiler<br>
<br>
Hi Shankar,<br>
<br>
I will answer the HaloProfiler related questions and leave the Hop questions<br>
for Stephen. However, could you post the failure output for what you tried<br>
to do with Hop. That will probably be helpful for answering your question.<br>
<br>
Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out<br>
> file ?<br>
><br>
<br>
Yes, the HaloProfiler will always use the same indices for halos as all of<br>
the halo finders in yt. So, the file Halo_N_profile.dat will always refer<br>
to halo N on the halo list.<br>
<br>
What is # ?<br>
><br>
<br>
This is just a comment character so that plotting programs don't try to read<br>
in what's on that line. The tab between it and the first field name is<br>
there to accommodate the routines that read those files back in to the<br>
HaloProfiler.<br>
<br>
<br>
> What is the meaning of ActualOverdensity ? And units ?<br>
><br>
<br>
ActualOverdensity has the same physical meaning as the regular Overdensity<br>
field. It is (Baryon Density + Dark Matter Density) / (Mean density of the<br>
universe). If you search the literature, you will find alternate<br>
definitions that use critical density instead of mean density. The one used<br>
here is a little more common (I think, but I'm not sure). As per these<br>
definitions, overdensity is a unitless quantity.<br>
<br>
In yt, there is an Overdensity field that is calculated on a cell-by-cell<br>
basis. For calculation of virial quantities for halos, the overdensity you<br>
calculate should be explicitly the total mass (baryon + dm) / total volume /<br>
mean density, where total refers to all cells enclosed within the sphere of<br>
the radial profile, not just the shell from r_(i-1) to r_i. Technically,<br>
you could get this by doing a profile of the Overdensity field, weighted by<br>
CellVolume, with accumulation set to True. However, if for some reason, the<br>
user wanted to do profiles of the overdensity field in a different way, say<br>
weighted by CellMass, or just counting the material shell-by-shell<br>
(accumulation=False), this number would not be correct for the calculation<br>
of virial quantities. For that reason, the HaloProfiler automatically<br>
generates this ActualOverdensity field which is assured to be calculated in<br>
the correct way. That way the user doesn't accidentally override a proper<br>
calculation of the overdensity used for the virial quantities.<br>
<br>
Other than the ActualOverdensity field (which is automatically generated by<br>
the HaloProfiler, and thus does not exist outside that context) you can<br>
always get the units of any field with:<br>
lagos.fieldInfo[some_field].units<br>
For more information, see here:<br>
<a href="http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-are" target="_blank">http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-are</a><br>
<br>
What is the meaning of CellVolume? And units ?<br>
<br>
What is Density referring to ? And units ?<br>
><br>
CellVolume and Density are the volume of a cell and the baryon density. In<br>
this context, they are the values of those fields in the radial profile. If<br>
you did it as per the recipe, the CellVolume is the total accumulated volume<br>
for all cells within the sphere radius. Density SHOULD be the<br>
mass-weighted, mean baryon density for cells within spherical shells.<br>
However, after looking at the recipe on the website, I see that, in error, I<br>
set the weight_field of the Density profile to None, instead of<br>
CellMassMsun. Therefore, the Density profile may be meaningless as is. I<br>
will change the recipe on the website ASAP.<br>
<br>
<br>
> What is mywieght ?<br>
><br>
<br>
The myweight field is a temporary field for keeping track of the weight<br>
field for a weight radial profile. It should be ignored and we might just<br>
want to not write it out in the future.<br>
<br>
<br>
> I also got the projection/ directory. But I got errors...<br>
><br>
<br>
It looks like the HaloProfiler tried to do a projection of Metallicity, but<br>
your simulation data did not have the MetalDensity field. You need to set<br>
CosmologyUseMetallicityField (or something like that) to 1 in your enzo<br>
parameter file in order to get this field. You can also just remove the<br>
line in the HaloProfiler recipe that adds the metallicity field to the list<br>
of projections.<br>
<br>
Cheers,<br>
<br>
Britton<br>
<br>
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<br></blockquote></div><br>