Mailman 3 March 2011 - yt-users

Re: [yt-users] 1D matter power spectrum
by Stephen Skory March 7, 2011

March 7, 2011

Geoffrey, > For each of the random point generated, I want to limit their position to > be on either the x, y or z direction instead of on a sphere, so I can > compare them with the 1D power spectrum. > > For example if I want to compare with the 1D powerspectrum along x, I want > phi = 0, theta= pi/2 > if I want to compare to z, then > phi = *, theta = pi/2 > > is this ability already in YT or can it be added easily? Ah, ok, now I understand. I can add this, … [View More]

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1D matter power spectrum
by gso＠physics.ucsd.edu March 7, 2011

March 7, 2011

Hi Stephen, I am trying to compare a 1D matter power spectrum from an IDL script. I was wondering when YT generates the random pts in tpf = TwoPointFunctions(pf, ['Density', 'CellVolume'], total_values=1e5, comm_size=10000, length_number=11, length_range=[-1, .5], length_type="lin", vol_ratio=1) is there a way to limit the random total_values of pts generated for say (r, theta, phi) in the physics convention? x = (phi = 0, theta = pi/2) y = (phi = pi/2, theta = pi/2) z = (phi = … [View More]

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Halo Loading
by Stephen Skory March 6, 2011

March 6, 2011

Hi All, due to popular demand, I've added functionality to load previously found halos off disk. It is in the "yt" branch of the repository. It should be easy to use, but may not be entirely free of bugs yet, so let me know if you have issues. To save the data: from yt.mods import * from yt.analysis_modules.halo_finding.api import * pf = load("data0005") haloes = HaloFinder(pf) haloes.dump("basename") basename is the root of the names for the files that will be saved on disk. So the text … [View More]

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Re: [yt-users] halos
by Stephen Skory March 5, 2011

March 5, 2011

Geoffrey, > Stephen, I would like to be able to calculate the a, b, c in the eqn of an > ellipsoid for the stars/dm particles in a Halo, and see how much mass is > in particles, and how much is in baryons. If I have the prescription to > do the calculation, can this be easily achieved if I have access to the > halo data if it was stored as binary in the .yt file? Or would this be > better done while it is still in memory with the halo profiler running? This is actually … [View More]

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Re: [yt-users] halos
by Stephen Skory March 4, 2011

March 4, 2011

Molly, > Right ... I spoke too soon, sorry. Now the halo profiler isn't > crashing, per se, but since I'm analyzing output in one of Matt's > directories, it's trying to save the HopAnalysis.out file to that > directory and can't, I think that unfortunately the HaloProfiler is hard-coded to save the HopAnalysis file to the data directory (Britton, am I wrong?). You can set the other output directories (look for profile_output_dir and projection_output_dir in http://yt.enzotools.… [View More]

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Re: [yt-users] halos
by Stephen Skory March 4, 2011

March 4, 2011

Molly Ok, I looked at the halo profiler bug and it's actually to do with the halo finder. So.... > /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc > in _run_finder(self) > 1056 self.particle_fields["particle_position_z"] / > self.period[2], > 1057 self.particle_fields["ParticleMassMsun"], > -> 1058 self.threshold) > 1059 … [View More]

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Re: [yt-users] halos
by Stephen Skory March 4, 2011

March 4, 2011

Molly, > Thanks for your quick reply. Unfortunately, the virial > information-getter is crashing in a different place now: > http://paste.enzotools.org/show/1522/ Argh. Sorry, it's another import error. Try updating (d0876afc8f08) and try again? Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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Re: [yt-users] halos
by Stephen Skory March 4, 2011

March 4, 2011

Irina, > If I understood correctly, what Molly wants is to read the HopAnalysis file to > get the halo information, since everything you know is in that file. But > isn't it already implemented in _read_halo_list in HaloProfiler.py (from an > older version of yt)? I think what Molly wants to do might be to find the haloes and than at some later point go back and look at detailed aspects of the haloes that aren't stored in the HopAnalysis.out file. For example, if she wants to … [View More]

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Re: [yt-users] halos
by Stephen Skory March 4, 2011

March 4, 2011

Molly, I can help you with the halos, but I'll leave the halo profiler for Britton who knows it better than I do. > First, I'm able to find halos and print information about them out to > an, e.g., HopAnalysis.out file. Is there a way to read this kind of > information back in? So far I have to re-run the halo finder every > time I want to get new information, which is rather inefficient. (The > kludge of only looking for halos in a subvolume where I know there is > one … [View More]

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halos
by Molly Peeples March 4, 2011

March 4, 2011

Hi all, I have a few questions/errors regarding halo analysis. First, I'm able to find halos and print information about them out to an, e.g., HopAnalysis.out file. Is there a way to read this kind of information back in? So far I have to re-run the halo finder every time I want to get new information, which is rather inefficient. (The kludge of only looking for halos in a subvolume where I know there is one kind of works but isn't ideal.) Second, virial information. When I try to get … [View More]the virial mass or radius I get errors like the following: In [12]: m_vir = halo.virial_mass() --------------------------------------------------------------------------- NameError Traceback (most recent call last) /home/molly-ucla/<ipython console> in <module>() /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in virial_mass(self, virial_overdensity, bins) 297 >>> vm = halos[0].virial_mass() 298 """ --> 299 self.virial_info(bins=bins) 300 vir_bin = self.virial_bin(virial_overdensity=virial_overdensity, bins=bins) 301 if vir_bin != -1: /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in virial_info(self, bins) 378 # can't see a way to eliminate a loop like this, either here or in 379 # yt.math. --> 380 for pos in izip(self["particle_position_x"], self["particle_position_y"], 381 self["particle_position_z"]): 382 dist[mark] = periodic_dist(cen, pos, period) NameError: global name 'izip' is not defined In [13]: r_vir = halo.virial_radius() --------------------------------------------------------------------------- NameError Traceback (most recent call last) /home/molly-ucla/<ipython console> in <module>() /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in virial_radius(self, virial_overdensity, bins) 331 >>> vr = halos[0].virial_radius() 332 """ --> 333 self.virial_info(bins=bins) 334 vir_bin = self.virial_bin(virial_overdensity=virial_overdensity, bins=bins) 335 if vir_bin != -1: /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in virial_info(self, bins) 378 # can't see a way to eliminate a loop like this, either here or in 379 # yt.math. --> 380 for pos in izip(self["particle_position_x"], self["particle_position_y"], 381 self["particle_position_z"]): 382 dist[mark] = periodic_dist(cen, pos, period) NameError: global name 'izip' is not defined But other derived quantities like, e.g., halo.rms_velocity(), work fine. (I'm running everything on SDSC's triton, fwiw.) Any ideas? Finally, I've been unable to get the halo profiler to work. I get errors such as: In [14]: import yt.analysis_modules.halo_profiler.api as HP In [15]: hp = HP.HaloProfiler(fn) yt : [INFO ] 2011-03-03 16:21:35,715 Parameters: current_time = 9.61651661575 yt : [INFO ] 2011-03-03 16:21:35,715 Parameters: domain_dimensions = [512, 512, 512] yt : [INFO ] 2011-03-03 16:21:35,715 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: cosmological_simulation = 1 yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: current_redshift = 18.3172950912 yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: omega_lambda = 0.721 yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: omega_matter = 0.279 yt : [INFO ] 2011-03-03 16:21:35,716 Parameters: hubble_constant = 0.701 yt : [INFO ] 2011-03-03 16:21:35,717 Hop file not found, running hop to get halos. yt : [INFO ] 2011-03-03 16:21:35,719 Getting particle_type using ParticleIO ['particle_type'] yt : [INFO ] 2011-03-03 16:22:43,486 Getting field particle_type from 1507 yt : [INFO ] 2011-03-03 16:23:16,501 Getting ParticleMassMsun using ParticleIO ['particle_type', 'particle_mass'] yt : [INFO ] 2011-03-03 16:24:03,160 Getting field ParticleMassMsun from 1507 yt : [INFO ] 2011-03-03 16:24:25,125 Initializing HOP yt : [INFO ] 2011-03-03 16:24:25,443 Getting particle_position_x using ParticleIO ['particle_type', 'particle_position_x', 'ParticleMassMsun', 'particle_mass'] yt : [INFO ] 2011-03-03 16:25:06,827 Getting field particle_position_x from 1507 yt : [INFO ] 2011-03-03 16:25:26,591 Getting particle_position_y using ParticleIO ['particle_type', 'particle_position_x', 'ParticleMassMsun', 'particle_mass', 'particle_position_y'] yt : [INFO ] 2011-03-03 16:26:14,612 Getting field particle_position_y from 1507 yt : [INFO ] 2011-03-03 16:26:25,516 Getting particle_position_z using ParticleIO ['particle_type', 'particle_position_z', 'particle_position_x', 'particle_position_y', 'ParticleMassMsun', 'particle_mass'] yt : [INFO ] 2011-03-03 16:27:17,495 Getting field particle_position_z from 1507 failed allocating particles. --------------------------------------------------------------------------- SystemError Traceback (most recent call last) /home/molly-ucla/<ipython console> in <module>() /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_profiler/multi_halo_profiler.pyc in __init__(self, dataset, halos, halo_list_file, halo_list_format, halo_finder_function, halo_finder_args, halo_finder_kwargs, use_density_center, density_center_exponent, use_field_max_center, halo_radius, radius_units, n_profile_bins, profile_output_dir, projection_output_dir, projection_width, projection_width_units, project_at_level, velocity_center, filter_quantities) 229 elif self.halos is 'multiple': 230 # Get hop data. --> 231 self._load_halo_data() 232 if len(self.all_halos) == 0: 233 mylog.error("No halos loaded, there will be nothing to do.") /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_profiler/multi_halo_profiler.pyc in _load_halo_data(self, filename) 578 if not(os.path.exists(hopFile)): 579 mylog.info("Hop file not found, running hop to get halos.") --> 580 self._run_hop(hopFile) 581 582 self.all_halos = self._read_halo_list(hopFile) /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_profiler/multi_halo_profiler.pyc in _run_hop(self, hopFile) 689 "Run hop to get halos." 690 --> 691 hop_results = self.halo_finder_function(self.pf, *self.halo_finder_args, **self.halo_finder_kwargs) 692 hop_results.write_out(hopFile) 693 /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in __init__(self, pf, subvolume, threshold, dm_only, padding) 1841 sub_mass = self._data_source["ParticleMassMsun"].sum(dtype='float64') 1842 HOPHaloList.__init__(self, self._data_source, -> 1843 threshold*total_mass/sub_mass, dm_only) 1844 self._parse_halolist(total_mass/sub_mass) 1845 self._join_halolists() /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in __init__(self, data_source, threshold, dm_only) 1048 self.threshold = threshold 1049 mylog.info("Initializing HOP") -> 1050 HaloList.__init__(self, data_source, dm_only) 1051 1052 def _run_finder(self): /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in __init__(self, data_source, dm_only) 801 self._max_dens = {} 802 self.__obtain_particles() --> 803 self._run_finder() 804 mylog.info("Parsing outputs") 805 self._parse_output() /home/molly-ucla/yt-x86_64/lib/python2.6/site-packages/yt-2.1dev-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.pyc in _run_finder(self) 1056 self.particle_fields["particle_position_z"] / self.period[2], 1057 self.particle_fields["ParticleMassMsun"], -> 1058 self.threshold) 1059 self.particle_fields["densities"] = self.densities 1060 self.particle_fields["tags"] = self.tags SystemError: error return without exception set (FWIW, I was using halos = HaloFinder(pf) previously to find halos.) The errors with both the virial information and halo profiler are reproducible, but I just re-ran everything with the latest release of yt so those are the errors you see. Any help/pointers would be appreciated. Thanks! --Molly [View Less]

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