<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Shankar and Britton,<div> 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).</div><div><br></div><div>cheers, </div><div><br></div><div><br><div><div>On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">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> <br>_______________________________________________<br> yt-users mailing list<br> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br> <br></blockquote></div><br> _______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org<br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Dr. Eric J. Hallman</div><div>NSF Astronomy and Astrophysics Postdoctoral Fellow </div><div>Center for Astrophysics and Space Astronomy </div><div>University of Colorado at Boulder </div><div>hallman (at) casa.colorado.edu </div><div>Phone: (312) 725-4626 </div><div><a href="http://solo.colorado.edu/~hallman/">http://solo.colorado.edu/~hallman/</a></div></div></div></span></div></span></div></span> </div><br></div></body></html>