Shankar,<div><br></div><div>Looks like I must have screwed up by a factor of four in my calculation earlier. So yeah, 1.25e12 should give you ~250 particles. Whether or not those objects are converged is another question, and something you'll have to investigate.</div>
<div><br></div><div>Sam</div><div><br></div><div><div class="gmail_quote">On Tue, Dec 8, 2009 at 7:25 PM, Agarwal, Shankar <span dir="ltr"><<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Eric and Sam,<br>
<br>
Yeah. that makes sense. It boils down to the resolution of the box.<br>
<br>
A question to Sam ... How did you get "mass resolution is about 2e10M_solar" ?<br>
<br>
I am getting 5e9M_solar as the mass of each dark matter particle. And the number of particles in a 1e13M_solar halo is 2000.<br>
<br>
ID mass particles density x y z centreofmass x centerofmass y centerofmass z<br>
3700 9.853250284e+12 2000 1.136880784e+04 3.619545698e-01 4.593685567e-01 8.036487699e-01 3.618929449e-01 4.593253520e-01 8.041266519e-01<br>
<br>
<br>
So I guess for 250 particles, I can try...<br>
<br>
virial_filters=[['TotalMassMsun','>=','1.25e12']]<br>
<br>
<br>
<br>
A question to Eric :<br>
<br>
Actually, I don't care for the resolution of the halos. I am analyzing the suppression of matter power spectrum as a function of neutrino mass. Which means I am interested only on the semi-linear scales of 20-60 Mpc/h. Towards this, I wish to extract small galaxy groups (upto 1e13M_solar) from my simulation. So, can I regard the HaloFinder halos as blobs, w/o caring for the resolution ? If yes, can I include halofinder halos with as low as 50-100 particles (since they are still halos, regardless of the resolution) ?<br>
<br>
I will appreciate if I can get some opinion on this.<br>
<font color="#888888"><br>
shankar<br>
</font><div><div></div><div class="h5"><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 Eric Hallman<br>
Sent: Tue 12/8/2009 4:53 PM<br>
To: Discussion of the yt analysis package<br>
Subject: Re: [yt-users] r_min in HaloProfiler<br>
<br>
Shankar,<br>
sam is right on the money with his analysis. Although the halo<br>
finders identify a large number of halos in your simulation they are<br>
very poorly resolved, and so this filter will rule them out on the<br>
basis of not getting to OD of 200. Our analysis with enzo shows that<br>
you can not expect the halos to be resolved under a few hundred<br>
particles as sam suggests.<br>
<br>
I would take a look at how many halos are above 500 particles or so<br>
and only run your analysis on those. I suspect it is possible that<br>
one of the reasons you are not seeing speedup with the parallel runs<br>
is that you don't have enough work for the processors given the small<br>
number of virialized halos that you'll actually analyze with this<br>
filter.<br>
<br>
<br>
On Dec 8, 2009, at 3:30 PM, Sam Skillman wrote:<br>
<br>
> Shankar,<br>
><br>
> In a box size of 200 Mpc/h^3 and 512^3 particles, your mass<br>
> resolution is about 2e10M_solar. That means in a 10^13 M_solar<br>
> halo, you have at most ~500 particles in your halos, which is well<br>
> resolved. The main problem with what you're doing is putting an<br>
> upper limit on the mass of the halos that you are profiling, which<br>
> is opposite to what one normally does. Even if you want to be<br>
> cavalier with what you call a halo, you definitely don't want to go<br>
> much below 2-5e12 since then you're talking 100 particles. I<br>
> personally don't trust profiles unless they have a few thousand<br>
> particles, because then I might believe the hydro is resolved. My<br>
> guess is that if you do:<br>
><br>
> virial_filters=[['TotalMassMsun','>=','5e12']]<br>
><br>
> you'll have more luck with them actually being virialized.<br>
><br>
> Main point:<br>
> If you want to study halos with masses less than 10^13, you're using<br>
> the wrong simulation (i.e. too large of a physical box size or too<br>
> small of a grid).<br>
><br>
> Sam<br>
><br>
><br>
> On Tue, Dec 8, 2009 at 3:04 PM, Agarwal, Shankar <<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>><br>
> wrote:<br>
> Sam,<br>
><br>
> I am trying to get the virial masses of the halos (with mass upto 1e<br>
> +13 Msun) with this 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','<=','1e13']],<br>
> virial_quantities=['TotalMassMsun','RadiusMpc'])<br>
><br>
><br>
> But when I look at the radial_profiles/Halo_xxxx_profile.dat files,<br>
> I see that none of the halos are virialized. The peak halo densities<br>
> are reaching about 20*mean_matter_density. I began my 200Mpc/h Box<br>
> with 512^3 particles simulation at z=99. I have not looked at the<br>
> literature in great detail but is there something fishy here ?<br>
><br>
><br>
> shankar<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 Sam Skillman<br>
> Sent: Tue 12/8/2009 3:23 PM<br>
> To: Discussion of the yt analysis package<br>
> Subject: Re: [yt-users] r_min in HaloProfiler<br>
><br>
> Shankar,<br>
><br>
> r_min is defined in your email:<br>
> r_min = 2 * self.pf.h.get_smallest_dx() * <a href="http://self.pf" target="_blank">self.pf</a>['mpc']<br>
><br>
> it's twice the smallest dx in units of mpc, dx being the smallest<br>
> cell size.<br>
> it is being rejected because your halo has something like 3 cells<br>
> (radial)<br>
> in it, which is almost certainly not resolved.<br>
><br>
> sam<br>
><br>
> On Tue, Dec 8, 2009 at 2:11 PM, Agarwal, Shankar <<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>><br>
> wrote:<br>
><br>
> > Hi,<br>
> ><br>
> > While running HaloProfiler, I am seeing this...<br>
> ><br>
> > P001 yt.lagos ERROR 2009-12-08 15:53:22,403 Skipping halo<br>
> with r_max<br>
> > / r_min = 1.885682.<br>
> ><br>
> ><br>
> ><br>
> > I looked at yt/extensions/HaloProfiler.py...<br>
> ><br>
> > r_min = 2 * self.pf.h.get_smallest_dx() * <a href="http://self.pf" target="_blank">self.pf</a>['mpc']<br>
> > if (halo['r_max'] / r_min < PROFILE_RADIUS_THRESHOLD):<br>
> > mylog.error("Skipping halo with r_max / r_min =<br>
> %f." %<br>
> > (halo['r_max']/r_min))<br>
> ><br>
> ><br>
> > r_max would be the distance to the furthest particle in the halo<br>
> as found<br>
> > by HaloFinder.<br>
> > But what is r_min ? And what is the basis for skipping this halo ?<br>
> ><br>
> ><br>
> > shankar<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>
><br>
><br>
><br>
> --<br>
> Samuel W. Skillman<br>
> DOE Computational Science Graduate Fellow<br>
> Center for Astrophysics and Space Astronomy<br>
> University of Colorado at Boulder<br>
> samuel.skillman[at]<a href="http://colorado.edu" target="_blank">colorado.edu</a><br>
><br>
><br>
> _______________________________________________<br>
> yt-users mailing list<br>
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><br>
><br>
><br>
><br>
> --<br>
> Samuel W. Skillman<br>
> DOE Computational Science Graduate Fellow<br>
> Center for Astrophysics and Space Astronomy<br>
> University of Colorado at Boulder<br>
> samuel.skillman[at]<a href="http://colorado.edu" target="_blank">colorado.edu</a><br>
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Eric Hallman<br>
Google Voice: (312) 725-HMAN<br>
<a href="mailto:hallman13@gmail.com">hallman13@gmail.com</a><br>
<br>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Samuel W. Skillman<br>DOE Computational Science Graduate Fellow<br>Center for Astrophysics and Space Astronomy<br>University of Colorado at Boulder<br>samuel.skillman[at]<a href="http://colorado.edu">colorado.edu</a><br>
</div>