<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Shankar,<div> sam is right on the money with his analysis. Although the halo finders identify a large number of halos in your simulation they are very poorly resolved, and so this filter will rule them out on the basis of not getting to OD of 200. Our analysis with enzo shows that you can not expect the halos to be resolved under a few hundred particles as sam suggests.</div><div><br></div><div>I would take a look at how many halos are above 500 particles or so and only run your analysis on those. I suspect it is possible that one of the reasons you are not seeing speedup with the parallel runs is that you don't have enough work for the processors given the small number of virialized halos that you'll actually analyze with this filter.</div><div><br></div><div><br><div><div>On Dec 8, 2009, at 3:30 PM, Sam Skillman wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Shankar,<div><br></div><div>In a box size of 200 Mpc/h^3 and 512^3 particles, your mass resolution is about 2e10M_solar. That means in a 10^13 M_solar halo, you have at most ~500 particles in your halos, which is well resolved. The main problem with what you're doing is putting an upper limit on the mass of the halos that you are profiling, which is opposite to what one normally does. Even if you want to be cavalier with what you call a halo, you definitely don't want to go much below 2-5e12 since then you're talking 100 particles. I personally don't trust profiles unless they have a few thousand particles, because then I might believe the hydro is resolved. My guess is that if you do:</div> <div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">virial_filters=[['TotalMassMsun','>=','5e12']]</span></div> <div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">you'll have more luck with them actually being virialized.</span></div> <div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div>Main point:</div><div>If you want to study halos with masses less than 10^13, you're using the wrong simulation (i.e. too large of a physical box size or too small of a grid). <br> <br></div><div>Sam</div><div><br></div><div><br><div class="gmail_quote">On Tue, Dec 8, 2009 at 3:04 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;"> Sam,<br> <br> I am trying to get the virial masses of the halos (with mass upto 1e+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, I see that none of the halos are virialized. The peak halo densities are reaching about 20*mean_matter_density. I began my 200Mpc/h Box with 512^3 particles simulation at z=99. I have not looked at the literature in great detail but is there something fishy here ?<br> <font color="#888888"><br> <br> shankar<br> </font><div><div></div><div class="h5"><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 cell size.<br> it is being rejected because your halo has something like 3 cells (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>> 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 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 = %f." %<br> > (halo['r_max']/r_min))<br> ><br> ><br> > r_max would be the distance to the furthest particle in the halo 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> </div></div><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 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> _______________________________________________<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 apple-content-edited="true"> <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; "><div>Eric Hallman</div><div>Google Voice: (312) 725-HMAN</div><div><a href="mailto:hallman13@gmail.com">hallman13@gmail.com</a></div><div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>