The overdensity in the profile is referring to dark matter + baryons. The field called "Density" is just baryon density.
The nans come from spherical shells of the radial profile that had nothing in them. If you look at the TotalMassMsun field, you'll notice that it is flat over the points where you get the nans and the value of myweight is 0.
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:<winmail.dat>_______________________________________________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 ?
From: firstname.lastname@example.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).
On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:Shankar,As I stated in my previous email, you will find both definitionsused in the literature. I'm not going to spend time in a citationbattle. The good news is that both definitions differ only by a
factor of Omega_matter, so you can change the value ofvirial_overdensity accordingly.BrittonOn Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <email@example.com>
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
Overdensityfield. It is (Baryon Density + Dark Matter Density) / (Meandensity of theuniverse). If you search the literature, you will find alternatedefinitions that use critical density instead of mean density. Theone usedhere 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...
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/0011495shankar-----Original Message-----From: firstname.lastname@example.org on behalf of Britton Smith
Sent: Wed 11/25/2009 1:30 PMTo: Discussion of the yt analysis packageSubject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,I will answer the HaloProfiler related questions and leave the Hop
questionsfor Stephen. However, could you post the failure output for whatyou triedto do with Hop. That will probably be helpful for answering yourquestion.Is Halo_0000_profile.dat related to the first Halo listed inHopAnalysis.outfile ?Yes, the HaloProfiler will always use the same indices for halos asall ofthe halo finders in yt. So, the file Halo_N_profile.dat will alwaysreferto halo N on the halo list.
What is # ?This is just a comment character so that plotting programs don't tryto readin what's on that line. The tab between it and the first field name
isthere to accommodate the routines that read those files back in to theHaloProfiler.What is the meaning of ActualOverdensity ? And units ?ActualOverdensity has the same physical meaning as the regularOverdensityfield. It is (Baryon Density + Dark Matter Density) / (Mean densityof theuniverse). If you search the literature, you will find alternate
definitions that use critical density instead of mean density. Theone usedhere is a little more common (I think, but I'm not sure). As per
thesedefinitions, overdensity is a unitless quantity.In yt, there is an Overdensity field that is calculated on a cell-by-
cellbasis. For calculation of virial quantities for halos, theoverdensity youcalculate should be explicitly the total mass (baryon + dm) / totalvolume /mean density, where total refers to all cells enclosed within the
sphere ofthe 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 byCellVolume, with accumulation set to True. However, if for some
reason, theuser wanted to do profiles of the overdensity field in a differentway, sayweighted by CellMass, or just counting the material shell-by-shell(accumulation=False), this number would not be correct for thecalculationof virial quantities. For that reason, the HaloProfiler automaticallygenerates this ActualOverdensity field which is assured to be
calculated inthe correct way. That way the user doesn't accidentally override apropercalculation of the overdensity used for the virial quantities.Other than the ActualOverdensity field (which is automatically
generated bythe HaloProfiler, and thus does not exist outside that context) youcanalways get the units of any field with:lagos.fieldInfo[some_field].unitsFor 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 baryondensity. In
this context, they are the values of those fields in the radialprofile. Ifyou did it as per the recipe, the CellVolume is the total
accumulated volumefor all cells within the sphere radius. Density SHOULD be themass-weighted, mean baryon density for cells within spherical shells.
However, after looking at the recipe on the website, I see that, inerror, Iset the weight_field of the Density profile to None, instead of
CellMassMsun. Therefore, the Density profile may be meaningless asis. Iwill change the recipe on the website ASAP.
What is mywieght ?The myweight field is a temporary field for keeping track of theweightfield for a weight radial profile. It should be ignored and wemight justwant 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 ofMetallicity, butyour simulation data did not have the MetalDensity field. You needto setCosmologyUseMetallicityField (or something like that) to 1 in your
enzoparameter file in order to get this field. You can also just removetheline in the HaloProfiler recipe that adds the metallicity field tothe listof projections.Cheers,Britton_______________________________________________yt-users mailing list_______________________________________________yt-users mailing list
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
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