[Yt-svn] commit/yt-doc: brittonsmith: Updated halo profiler doc.

[Bitbucket]

1 new changeset in yt-doc:

http://bitbucket.org/yt_analysis/yt-doc/changeset/b2df369549f4/
changeset:   r34:b2df369549f4
user:        brittonsmith
date:        2011-03-05 19:46:02
summary:     Updated halo profiler doc.
affected #:  1 file (151 bytes)

--- a/source/analysis_modules/halo_profiling.rst	Fri Mar 04 14:40:30 2011 -0500
+++ b/source/analysis_modules/halo_profiling.rst	Sat Mar 05 13:46:02 2011 -0500
@@ -4,34 +4,36 @@
 ==============
 .. sectionauthor:: Britton Smith <britton.smith at colorado.edu>
 
-The HaloProfiler provides a means of performing analysis on multiple points in a dataset at 
+The halo profiler provides a means of performing analysis on multiple points in a dataset at 
 once.  This is primarily intended for use with cosmological simulations, in which  
 gravitationally bound structures composed of dark matter and gas, called halos, form and 
 become the hosts for galaxies and galaxy clusters.
 
-The HaloProfiler performs two primary functions: radial profiles and projections.  
-With only a few exceptions discussed below, all of the HaloProfiler's machinery can 
+The halo profiler performs two primary functions: radial profiles and projections.  
+With only a few exceptions discussed below, all of the halo profiler's machinery can 
 be run in parallel, with `mpi4py <http://code.google.com/p/mpi4py/>`_ installed, by running 
 your script inside an mpirun call with the --parallel flag at the end.
 
-Configuring the HaloProfiler
+Configuring the Halo Profiler
 ----------------------------
 
-A sample script to run the HaloProfiler can be found in :ref:`cookbook-run_halo_profiler`.  
-In order to run the HaloProfiler on a dataset, a HaloProfiler object must be instantiated 
+A sample script to run the halo profiler can be found in :ref:`cookbook-run_halo_profiler`.  
+In order to run the halo profiler on a dataset, a halo profiler object must be instantiated 
 with the path to the dataset as the only argument:
 
 .. code-block:: python
 
   import yt.analysis_modules.halo_profiler.api as HP
-  hp = HP.HaloProfiler("DD0242/DD0242")
+  hp = HP.halo_profiler("DD0242/DD0242")
 
-Most of the HaloProfiler's options are configured with keyword arguments given at 
+Most of the halo profiler's options are configured with keyword arguments given at 
 instantiation.  These options are:
 
+ * **output_dir** (*str*): if specified, all output will be put into this path instead of in the dataset directories.  Default: None.
+
  * **halos** (*str*): "multiple" for profiling more than one halo.  In this mode halos are read in from a list or identified with a `halo finder <../cookbook/running_halofinder.html>`_.  In "single" mode, the one and only halo center is identified automatically as the location of the peak in the density field.  Default: "multiple".
 
- * **halo_list_file** (*str*): name of file containing the list of halos.  The HaloProfiler will look for this file in the data directory.  Default: "HopAnalysis.out".
+ * **halo_list_file** (*str*): name of file containing the list of halos.  The halo profiler will look for this file in the data directory.  Default: "HopAnalysis.out".
 
  * **halo_list_format** (*str* or *dict*): the format of the halo list file.  "yt_hop" for the format given by yt's halo finders.  "enzo_hop" for the format written by enzo_hop.  This keyword can also be given in the form of a dictionary specifying the column in which various properties can be found.  For example, {"id": 0, "center": [1, 2, 3], "mass": 4, "radius": 5}.  Default: "yt_hop".
 
@@ -70,12 +72,12 @@
 
  * **filter_quantities** (*list*): quantities from the original halo list file to be written out in the filtered list file.  Default: ['id','center'].
 
-.. warning:: The HaloProfiler runs in parallel in a round-robin style, evenly distributing the list of halos among all processors.  Hence, the HaloProfiler will not work in parallel when **halos** is set to single.
+.. warning:: The halo profiler runs in parallel in a round-robin style, evenly distributing the list of halos among all processors.  Hence, the halo profiler will not work in parallel when **halos** is set to single.
 
 Profiles
 --------
 
-Once the HaloProfiler object has been instantiated, fields can be added for profiling with 
+Once the halo profiler object has been instantiated, fields can be added for profiling with 
 the :meth:`add_profile` method:
 
 .. code-block:: python
@@ -152,7 +154,7 @@
 The addition above will calculate and return virial quantities, mass and radius, for an 
 overdensity of 200.  In order to pass the filter, at least one point in the profile must be 
 above the specified overdensity and the virial mass must be at least 1e14 solar masses.  If 
-the VirialFilter function has been added to the filter list, the HaloProfiler will make 
+the VirialFilter function has been added to the filter list, the halo profiler will make 
 sure that the fields necessary for calculating virial quantities are added.  As 
 many filters as desired can be added.  If filters have been added, the next call to 
 :meth:`make_profiles` will filter by all of the added filter functions:
@@ -164,7 +166,7 @@
 If the **filename** keyword is set, a file will be written with all of the filtered halos 
 and the quantities returned by the filter functions.
 
-.. note:: If the profiles have already been run, the HaloProfiler will read in the previously created output files instead of re-running the profiles.  The HaloProfiler will check to make sure the output file contains all of the requested halo fields.  If not, the profile will be made again from scratch.
+.. note:: If the profiles have already been run, the halo profiler will read in the previously created output files instead of re-running the profiles.  The halo profiler will check to make sure the output file contains all of the requested halo fields.  If not, the profile will be made again from scratch.
 
 .. _halo_profiler_pre_filters:

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

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