[yt-svn] commit/yt-doc: 2 new changesets

[Bitbucket]

2 new commits in yt-doc:

https://bitbucket.org/yt_analysis/yt-doc/commits/7920588095ae/
changeset:   7920588095ae
user:        chummels
date:        2013-02-15 23:53:37
summary:     Adding information and a recipe on how to do halo tracking with halo_merger_tree.
affected #:  2 files

diff -r 3ce56a80b3c34b3ab60c9cbc8dccb0b7c202538c -r 7920588095ae3d928f2ed6190fef1c021b9a514b source/cookbook/cosmological_analysis.rst
--- a/source/cookbook/cosmological_analysis.rst
+++ b/source/cookbook/cosmological_analysis.rst
@@ -40,6 +40,14 @@
 1) radial profiles and filtering; 2) projections; and 3) custom halo 
 analysis.
 
+.. yt_cookbook:: halo_merger_tree.py
+
+Halo Tracking Across Timesteps
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+This script demonstrates tracking a halo across multiple timesteps
+in a TimeSeries object, as well as some handy functions for looking
+at the properties of that halo over time.
+
 .. yt_cookbook:: halo_profiler.py
 
 Light Cone Projection

diff -r 3ce56a80b3c34b3ab60c9cbc8dccb0b7c202538c -r 7920588095ae3d928f2ed6190fef1c021b9a514b source/cookbook/halo_merger_tree.py
--- /dev/null
+++ b/source/cookbook/halo_merger_tree.py
@@ -0,0 +1,72 @@
+# This script demonstrates some of the halo merger tracking infrastructure,
+# for tracking halos across multiple datadumps in a time series.
+# Ultimately, it outputs an HDF5 file with the important quantities for the
+# top 20 most massive halos in the datadump, and it plots out their mass
+# accretion histories to a series of plots.
+
+# Currently this has only been tested with enzo outputs, but we are looking
+# to generalize this with other codes imminently.
+
+from yt.mods import *
+from yt.analysis_modules.halo_finding.api import *
+from yt.analysis_modules.halo_merger_tree.api import *
+
+# Makes a TimeSeries object from all of whatever files you have
+ts = TimeSeriesData.from_filenames("DD????/DD????")
+
+# For each datadump in our timeseries, run the friends of friends
+# halo finder on it (this has only been tested with FOF currently).
+# Output the information about the halos and the particles comprising each
+# to disk.  These files will all be in the FOF subdirectory.
+# This also works with an external FOF program run outside of yt,
+# in which case skip this step and do that yourself.
+
+# ------------------------------------------------------------
+# DEPENDING ON THE SIZE OF YOUR FILES, THIS CAN BE A LONG STEP 
+# but because we're writing them out to disk, you only have to do this once.
+# ------------------------------------------------------------
+for pf in ts:
+    halo_list = FOFHaloFinder(pf)
+    i = int(pf.basename[2:])
+    halo_list.write_out("FOF/groups_%05i.txt" % i)
+    halo_list.write_particle_lists("FOF/particles_%05i" % i)
+
+# Create a merger tree object.  This object is a tuple, where the
+# first part is a dictionary showing the correlation between file 
+# output_number and redshift.  The second part is a dictionary
+# correlating each halo with it's parent halos from the previous timestep
+# (along with number and fraction of particles taken from that parent)
+
+# ------------------------------------------------------------
+# DEPENDING ON THE SIZE OF YOUR FILES, THIS CAN BE A LONG STEP 
+# but because we're writing them out to disk, you only have to do this once.
+# ------------------------------------------------------------
+
+# by default, this saves the merger tree to disk in a CPickle:
+# FOF/merger_tree.cpkl so you can use it later.
+# Note that there are a bunch of filters you can place on this, so 
+# that you're only building a merger tree for a subset of redshifts
+# or data outputs.
+mt = EnzoFOFMergerTree(external_FOF=False)
+
+# If you want to just use your already generated merger_tree, 
+# uncomment the next line.
+# mt = EnzoFOFMergerTree(external_FOF=False, load_saved=True)
+
+# For each of the top 20 most massive halos from the final timestep
+# build its merger history.  You can then print this tree to screen, 
+# or more usefully, save the lineage of that tree to disk for use 
+# later.  save_halo_evolution() follows the largest progenitor
+# which contributes the most to the subsequent children.
+for i in range(20):
+    mt.build_tree(i)
+    mt.print_tree()
+    mt.save_halo_evolution('halos.h5')
+
+# For each of the top 20 most massive halos from the final timestep
+# plot its evolution of two quantities.  The default is to look at 
+# timestep vs mass, but you can look at center_of_mass phase-space 
+# coordinates, fraction from progenitor, mass of halo, and more.
+# These are spit out to .png files in the FOF directory.
+for i in range(20):
+    plot_halo_evolution('halos.h5', i)


https://bitbucket.org/yt_analysis/yt-doc/commits/ecd29bc6c175/
changeset:   ecd29bc6c175
user:        chummels
date:        2013-02-16 00:04:05
summary:     Fixing ordering.
affected #:  1 file

diff -r 7920588095ae3d928f2ed6190fef1c021b9a514b -r ecd29bc6c175165605481462f09ab3bcadafe41d source/cookbook/cosmological_analysis.rst
--- a/source/cookbook/cosmological_analysis.rst
+++ b/source/cookbook/cosmological_analysis.rst
@@ -40,7 +40,7 @@
 1) radial profiles and filtering; 2) projections; and 3) custom halo 
 analysis.
 
-.. yt_cookbook:: halo_merger_tree.py
+.. yt_cookbook:: halo_profiler.py
 
 Halo Tracking Across Timesteps
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -48,7 +48,7 @@
 in a TimeSeries object, as well as some handy functions for looking
 at the properties of that halo over time.
 
-.. yt_cookbook:: halo_profiler.py
+.. yt_cookbook:: halo_merger_tree.py
 
 Light Cone Projection
 ~~~~~~~~~~~~~~~~~~~~~

Repository URL: https://bitbucket.org/yt_analysis/yt-doc/

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