<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Shankar,<div> to your second point. The whole issue about resolution (mass resolution that is) is that unless the potential is resolved, you can't be sure if a) it is a real halo or just a chance aggregation of particles, and b) you certainly can't say you know it's mass accurately. In a statistical sense, you have some halo mass function down to 50 or so particles and that is ok, but for any individual halos, their properties are NOT accurately represented in the simulation at this level of mass resolution. </div><div><br></div><div><br><div><div>On Dec 8, 2009, at 7:25 PM, Agarwal, Shankar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>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><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 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><blockquote type="cite">Shankar,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In a box size of 200 Mpc/h^3 and 512^3 particles, your mass <br></blockquote><blockquote type="cite">resolution is about 2e10M_solar. That means in a 10^13 M_solar <br></blockquote><blockquote type="cite">halo, you have at most ~500 particles in your halos, which is well <br></blockquote><blockquote type="cite">resolved. The main problem with what you're doing is putting an <br></blockquote><blockquote type="cite">upper limit on the mass of the halos that you are profiling, which <br></blockquote><blockquote type="cite">is opposite to what one normally does. Even if you want to be <br></blockquote><blockquote type="cite">cavalier with what you call a halo, you definitely don't want to go <br></blockquote><blockquote type="cite">much below 2-5e12 since then you're talking 100 particles. I <br></blockquote><blockquote type="cite">personally don't trust profiles unless they have a few thousand <br></blockquote><blockquote type="cite">particles, because then I might believe the hydro is resolved. My <br></blockquote><blockquote type="cite">guess is that if you do:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">virial_filters=[['TotalMassMsun','>=','5e12']]<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">you'll have more luck with them actually being virialized.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Main point:<br></blockquote><blockquote type="cite">If you want to study halos with masses less than 10^13, you're using <br></blockquote><blockquote type="cite">the wrong simulation (i.e. too large of a physical box size or too <br></blockquote><blockquote type="cite">small of a grid).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Sam<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Tue, Dec 8, 2009 at 3:04 PM, Agarwal, Shankar <<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>> <br></blockquote><blockquote type="cite">wrote:<br></blockquote><blockquote type="cite">Sam,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am trying to get the virial masses of the halos (with mass upto 1e <br></blockquote><blockquote type="cite">+13 Msun) with this filter...<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">hp.add_halo_filter(HP.VirialFilter, must_be_virialized=True,<br></blockquote><blockquote type="cite"> overdensity_field='ActualOverdensity',<br></blockquote><blockquote type="cite"> virial_overdensity=200,<br></blockquote><blockquote type="cite"> virial_filters=[['TotalMassMsun','<=','1e13']],<br></blockquote><blockquote type="cite"> virial_quantities=['TotalMassMsun','RadiusMpc'])<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">But when I look at the radial_profiles/Halo_xxxx_profile.dat files, <br></blockquote><blockquote type="cite">I see that none of the halos are virialized. The peak halo densities <br></blockquote><blockquote type="cite">are reaching about 20*mean_matter_density. I began my 200Mpc/h Box <br></blockquote><blockquote type="cite">with 512^3 particles simulation at z=99. I have not looked at the <br></blockquote><blockquote type="cite">literature in great detail but is there something fishy here ?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">shankar<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----Original Message-----<br></blockquote><blockquote type="cite">From: <a href="mailto:yt-users-bounces@lists.spacepope.org">yt-users-bounces@lists.spacepope.org</a> on behalf of Sam Skillman<br></blockquote><blockquote type="cite">Sent: Tue 12/8/2009 3:23 PM<br></blockquote><blockquote type="cite">To: Discussion of the yt analysis package<br></blockquote><blockquote type="cite">Subject: Re: [yt-users] r_min in HaloProfiler<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Shankar,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">r_min is defined in your email:<br></blockquote><blockquote type="cite">r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc']<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">it's twice the smallest dx in units of mpc, dx being the smallest <br></blockquote><blockquote type="cite">cell size.<br></blockquote><blockquote type="cite"> it is being rejected because your halo has something like 3 cells <br></blockquote><blockquote type="cite">(radial)<br></blockquote><blockquote type="cite">in it, which is almost certainly not resolved.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">sam<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Tue, Dec 8, 2009 at 2:11 PM, Agarwal, Shankar <<a href="mailto:sagarwal@ku.edu">sagarwal@ku.edu</a>> <br></blockquote><blockquote type="cite">wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">While running HaloProfiler, I am seeing this...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">P001 yt.lagos ERROR 2009-12-08 15:53:22,403 Skipping halo <br></blockquote></blockquote><blockquote type="cite">with r_max<br></blockquote><blockquote type="cite"><blockquote type="cite">/ r_min = 1.885682.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I looked at yt/extensions/HaloProfiler.py...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc']<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> if (halo['r_max'] / r_min < PROFILE_RADIUS_THRESHOLD):<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> mylog.error("Skipping halo with r_max / r_min = <br></blockquote></blockquote><blockquote type="cite">%f." %<br></blockquote><blockquote type="cite"><blockquote type="cite">(halo['r_max']/r_min))<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">r_max would be the distance to the furthest particle in the halo <br></blockquote></blockquote><blockquote type="cite">as found<br></blockquote><blockquote type="cite"><blockquote type="cite">by HaloFinder.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">But what is r_min ? And what is the basis for skipping this halo ?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">shankar<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">yt-users mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Samuel W. Skillman<br></blockquote><blockquote type="cite">DOE Computational Science Graduate Fellow<br></blockquote><blockquote type="cite">Center for Astrophysics and Space Astronomy<br></blockquote><blockquote type="cite">University of Colorado at Boulder<br></blockquote><blockquote type="cite">samuel.skillman[at]colorado.edu<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">yt-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">Samuel W. Skillman<br></blockquote><blockquote type="cite">DOE Computational Science Graduate Fellow<br></blockquote><blockquote type="cite">Center for Astrophysics and Space Astronomy<br></blockquote><blockquote type="cite">University of Colorado at Boulder<br></blockquote><blockquote type="cite">samuel.skillman[at]colorado.edu<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">yt-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote><br>Eric Hallman<br>Google Voice: (312) 725-HMAN<br><a href="mailto:hallman13@gmail.com">hallman13@gmail.com</a><br><br><br><br><br><span><winmail.dat></span>_______________________________________________<br>yt-users mailing list<br>yt-users@lists.spacepope.org<br>http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org<br></div></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>