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

Bitbucket commits-noreply at bitbucket.org
Wed Jun 20 11:37:57 PDT 2012 

2 new commits in yt-doc:


https://bitbucket.org/yt_analysis/yt-doc/changeset/20cbad486d13/
changeset:   20cbad486d13
user:        gsiisg
date:        2012-06-20 03:12:32
summary:     added in ellipsoid stuff to analysis_modules
affected #:  1 file

diff -r 7f02f51bde8a1cccafa3743223df4017c0b809be -r 20cbad486d13652aadd35639627ea434c527182d source/analysis_modules/index.rst
--- a/source/analysis_modules/index.rst
+++ b/source/analysis_modules/index.rst
@@ -21,3 +21,4 @@
    clump_finding
    radial_column_density
    sunrise_export
+   ellipsoid_analysis



https://bitbucket.org/yt_analysis/yt-doc/changeset/227dded5947a/
changeset:   227dded5947a
user:        gsiisg
date:        2012-06-20 11:59:23
summary:     added missing file
affected #:  1 file

diff -r 20cbad486d13652aadd35639627ea434c527182d -r 227dded5947a1b6a819d743f6decb57a7ab9bebd source/analysis_modules/ellipsoid_analysis.rst
--- /dev/null
+++ b/source/analysis_modules/ellipsoid_analysis.rst
@@ -0,0 +1,164 @@
+.. _ellipsoid_analysis:
+
+Halo Ellipsoid Analysis
+===============
+.. sectionauthor:: Geoffrey So <gso at physics.ucsd.edu>
+
+.. warning:: This is my first attempt at modifying the YT source code,
+   so the program may be bug ridden.  Please send yt-dev an email and
+   address to Geoffrey So if you discover something wrong with this
+   portion of the code.
+
+Purpose
+-------
+
+The purpose of creating this feature in YT is to analyze field
+properties that surrounds the dark matter halo.  Originally, this was
+usually done with the sphere 3D container, but since many halo
+particles are linked together in a more elongated shape, I thought it
+would be better to use an ellipsoid 3D container to wrap around the
+particles.  This way less of the empty-of-particle space around the
+halo would be included when doing the analysis of field properties
+where the particles are suppose to occupy.
+
+General Overview
+--------------
+
+In order to use the ellipsoid 3D container object, one must supply it
+with a center, the magnitude of the semi-principle axes, the direction
+of the first semi-principle axis, the tilt angle (rotation angle about
+the y axis that will align the first semi-principle axis with the x
+axis once it is aligned in the x-z plane.)
+
+Once those parameters are determines, the function "ellipsoid" will
+return the 3D object, and users will be able to get field attributes
+from the data object just they would from spheres, cylinders etc.
+
+Example
+-------
+
+To use the ellipsoid container to get field information, you
+will have to first determine the ellipsoid's parameters.  This can be
+done with the haloes obtained from halo finding, but essentially it
+takes the informaton:
+
+  #. Center position x,y,z
+  #. List of particles position x,y,z
+
+And calculates the ellipsoid information needed for the 3D container.
+
+What I usually do is get this information from the halo finder output
+files in the .h5 HDF5 binary format. I load them in using the
+LoadHaloes() function instead of reading in the ASCII output.
+
+Halo Finding:
+~~~~~~~~~~~
+.. code-block:: python
+
+  from yt.mods import *
+  from yt.analysis_modules.halo_finding.api import *
+
+  pf=load('RD0006/RD0006')
+  halo_list = parallelHF(pf)
+  halo_list.dump('MyHaloList')
+
+Ellipsoid Parameters:
+~~~~~~~~~~~~~~~~~
+.. code-block:: python
+
+  from yt.mods import *
+  from yt.analysis_modules.halo_finding.api import *
+
+  pf=load('RD0006/RD0006')
+  haloes = LoadHaloes(pf, 'MyHaloList')
+
+Once the halo information is saved you can load it into the data
+object haloes, you can get loop over the list of haloes and do
+
+.. code-block:: python
+
+  ell_param = haloes[0].get_ellipsoid_parameters()
+
+This will return 6 items
+
+  #. The center of mass as an array.
+  #. A as a float.
+  #. B as a float.
+  #. C as a float.
+  #. e0 vector as an array.
+  #. tilt as a float.
+
+The center of mass would be the same one as returned by the halo
+finder.  The A, B, C are the largest to smallest magnitude of the
+ellipsoid's semi-principle axes. "e0" is the largest semi-principle
+axis vector direction that would have magnitude A but normalized.  The
+"tilt" is an angle in radians. It is the rotation angle needed to align the
+medium semi-principle axis with the y axis in the x-z plane, AFTER the
+e0 axis is aligned with the x-axis in the x-y plane by rotation, then
+aligned again in the x-z plane by rotation.
+
+Ellipsoid 3D Container
+~~~~~~~~~~~~~~~~~~
+
+Once the parameters are obtained from the get_ellipsoid_parameters()
+function, or picked at random by the user, it can be input into the
+ellipsoid container as:
+
+.. code-block:: python
+
+  ell = pf.h.ellipsoid(ell_param[0],
+  ell_param[1],
+  ell_param[2],
+  ell_param[3],
+  ell_param[4],
+  ell_param[5])
+  dens = ell.quantities['TotalQuantity']('Density')[0]
+
+This way, "ell" will be the ellipsoid container, and "dens" will be
+the total density of the ellipsoid in an unigrid simulation.  One can
+of course use this container object with parameters that they come up
+with, the ellipsoid parameters do not have to come from the Halo
+Finder.  And of course, one can use the ellipsoid container with other
+derived fields or fields that they are interested in.
+
+Drawbacks
+---------
+
+Since this is a first attempt, there are many drawbacks and corners
+cut.  Many things listed here will be amended when I have time.
+
+* The ellipsoid 3D container like the boolean object, do not contain 
+  particle position and velocity information.
+* This currently assume periodic boundary condition, so if an
+  ellipsoid center is at the edge, it will return part of the opposite
+  edge field information.  Will try to put in the option to turn off
+  periodicity in the future.
+* This method gives a minimalistic ellipsoid centered around the
+  center of mass that contains all the particles, but sometimes people
+  prefer an inertial tensor triaxial ellipsoid described in 
+  `Dubinski, Carlberg 1991
+  <http://adsabs.harvard.edu/abs/1991ApJ...378..496D>`_.  I have that
+  method composed but it is not fully tested yet.
+* The method to obtain information from the halo still uses the center
+  of mass as the center of the ellipsoid, so it is not making the
+  smallest ellipsoid that contains the particles as possible.  To
+  start at the center of the particles based on position will require
+  an O(:math:`N^2`) operation, right now I'm trying to limit
+  everything to O(:math:`N`) operations.
+* Currently the list of haloes can be analyzed using object
+  parallelism (one halo per core), but I'm not sure if haloes will get
+  big enough soon that other forms of parallelism will be needed to
+  analyze them due to memory constraint.
+* This has only been tested on unigrid simulation data, not AMR.  In
+  unigrid simulations, I can take "dens" from the example and divide
+  it by the total number of cells to get the average density, in AMR
+  one would need to do an volume weighted average instead.
+
+Thanks
+------
+
+Big thanks to the yt-user and yt-dev community that have been so
+supportive.  Special thanks to Stephen Skory for help in coding some
+functions that I'm not familiar with, Britton Smith's advice to shave
+off redundant data, Matt Turk for encouraging me to even start on
+this trek, and Dave Collins for getting ideas straight in my head.

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