[Yt-svn] yt-commit r1766 - trunk/yt/lagos
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Fri Jun 25 16:39:32 PDT 2010
Author: mturk
Date: Fri Jun 25 16:39:31 2010
New Revision: 1766
URL: http://yt.enzotools.org/changeset/1766
Log:
Fixing docstrings that wouldn't compile, added the summary section, fixed
periodicity in a few places.
Modified:
trunk/yt/lagos/HaloFinding.py
Modified: trunk/yt/lagos/HaloFinding.py
==============================================================================
--- trunk/yt/lagos/HaloFinding.py (original)
+++ trunk/yt/lagos/HaloFinding.py Fri Jun 25 16:39:31 2010
@@ -84,9 +84,11 @@
def center_of_mass(self):
r"""Calculate and return the center of mass.
+
+ The center of mass of the halo is directly calculated and returned.
Examples
- -------
+ --------
>>> com = halos[0].center_of_mass()
"""
c_vec = self.maximum_density_location() - na.array([0.5,0.5,0.5])
@@ -100,9 +102,11 @@
def maximum_density(self):
r"""Return the HOP-identified maximum density. Not applicable to
FOF halos.
-
+
+ Return the HOP-identified maximum density. Not applicable to FOF halos.
+
Examples
- -------
+ --------
>>> max_dens = halos[0].maximum_density()
"""
return self._max_dens[self.id][0]
@@ -110,9 +114,11 @@
def maximum_density_location(self):
r"""Return the location HOP identified as maximally dense. Not
applicable to FOF halos.
-
+
+ Return the location HOP identified as maximally dense.
+
Examples
- -------
+ --------
>>> max_dens_loc = halos[0].maximum_density_location()
"""
return na.array([
@@ -123,14 +129,20 @@
def total_mass(self):
r"""Returns the total mass in solar masses of the halo.
+ Returns the total mass in solar masses of just the particles in the
+ halo.
+
Examples
- -------
+ --------
>>> halos[0].total_mass()
"""
return self["ParticleMassMsun"].sum()
def bulk_velocity(self):
r"""Returns the mass-weighted average velocity in cm/s.
+
+ This calculates and returns the mass-weighted average velocity of just
+ the particles in the halo in cm/s.
Examples
--------
@@ -145,6 +157,10 @@
def rms_velocity(self):
r"""Returns the mass-weighted RMS velocity for the halo
particles in cgs units.
+
+ Calculate and return the mass-weighted RMS velocity for just the
+ particles in the halo. The bulk velocity of the halo is subtracted
+ before computation.
Examples
--------
@@ -164,10 +180,13 @@
r"""Returns the maximum radius in the halo for all particles,
either from the point of maximum density or from the
center of mass.
+
+ The maximum radius from the most dense point is calculated. This
+ accounts for periodicity.
Parameters
- ---------
- center_of_mass : Boolean
+ ----------
+ center_of_mass : bool
True chooses the center of mass when calculating the maximum radius.
False chooses from the maximum density location for HOP halos
(it has no effect for FOF halos).
@@ -182,9 +201,10 @@
rx = na.abs(self["particle_position_x"]-center[0])
ry = na.abs(self["particle_position_y"]-center[1])
rz = na.abs(self["particle_position_z"]-center[2])
- r = na.sqrt(na.minimum(rx, 1.0-rx)**2.0
- + na.minimum(ry, 1.0-ry)**2.0
- + na.minimum(rz, 1.0-rz)**2.0)
+ DW = self.data.pf["DomainRightEdge"] - self.data.pf["DomainLeftEdge"]
+ r = na.sqrt(na.minimum(rx, DW[0]-rx)**2.0
+ + na.minimum(ry, DW[1]-ry)**2.0
+ + na.minimum(rz, DW[2]-rz)**2.0)
return r.max()
def __getitem__(self, key):
@@ -194,17 +214,24 @@
return self.data[key][self.indices]
def get_sphere(self, center_of_mass=True):
- r"""Returns an EnzoSphere centered on either the point of maximum density
- or the center of mass, with the maximum radius of the halo.
+ r"""Returns a sphere source.
+
+ This will generate a new, empty sphere source centered on this halo,
+ with the maximum radius of the halo.
Parameters
----------
- center_of_mass : Boolean
+ center_of_mass : bool, optional
True chooses the center of mass when calculating the maximum radius.
False chooses from the maximum density location for HOP halos
(it has no effect for FOF halos).
Default = True.
+ Returns
+ -------
+ sphere : `yt.lagos.AMRSphereBase`
+ The empty data source.
+
Examples
--------
>>> sp = halos[0].get_sphere()
@@ -234,17 +261,25 @@
def virial_mass(self, virial_overdensity=200., bins=300):
r"""Return the virial mass of the halo in Msun, using only the particles
- in the halo (no baryonic information used). Returns -1 if the halo is
- not virialized.
+ in the halo (no baryonic information used).
+
+ The virial mass is calculated, using the built in `Halo.virial_info`
+ functionality. The mass is then returned.
Parameters
----------
- virial_overdensity : Float
+ virial_overdensity : float
The overdensity threshold compared to the universal average when
calculating the virial mass. Default = 200.
- bins : Integer
+ bins : int
The number of spherical bins used to calculate overdensities.
Default = 300.
+
+ Returns
+ -------
+ mass : float
+ The virial mass in solar masses of the particles in the halo. -1
+ if not virialized.
Examples
--------
@@ -259,18 +294,26 @@
def virial_radius(self, virial_overdensity=200., bins=300):
- r"""Return the virial radius of the halo in code units, using only the
- particles in the halo (no baryonic information used). Returns -1 if the
- halo is not virialized.
+ r"""Return the virial radius of the halo in code units.
+
+ The virial radius of the halo is calculated, using only the particles
+ in the halo (no baryonic information used). Returns -1 if the halo is
+ not virialized.
Parameters
----------
- virial_overdensity : Float
+ virial_overdensity : float
The overdensity threshold compared to the universal average when
calculating the virial radius. Default = 200.
- bins : Integer
+ bins : integer
The number of spherical bins used to calculate overdensities.
Default = 300.
+
+ Returns
+ -------
+ radius : float
+ The virial raius in code units of the particles in the halo. -1
+ if not virialized.
Examples
--------
@@ -358,9 +401,11 @@
def maximum_density(self):
r"""Return the HOP-identified maximum density.
-
+
+ Return the HOP-identified maximum density.
+
Examples
- -------
+ --------
>>> max_dens = halos[0].maximum_density()
"""
if self.max_dens_point is not None:
@@ -371,8 +416,10 @@
def maximum_density_location(self):
r"""Return the location HOP identified as maximally dense.
+ Return the location HOP identified as maximally dense.
+
Examples
- -------
+ --------
>>> max_dens_loc = halos[0].maximum_density_location()
"""
if self.max_dens_point is not None:
@@ -392,9 +439,11 @@
def center_of_mass(self):
r"""Calculate and return the center of mass.
+
+ The center of mass of the halo is directly calculated and returned.
Examples
- -------
+ --------
>>> com = halos[0].center_of_mass()
"""
# If it's precomputed, we save time!
@@ -421,8 +470,11 @@
def total_mass(self):
r"""Returns the total mass in solar masses of the halo.
+ Returns the total mass in solar masses of just the particles in the
+ halo.
+
Examples
- -------
+ --------
>>> halos[0].total_mass()
"""
if self.group_total_mass is not None:
@@ -436,6 +488,9 @@
def bulk_velocity(self):
r"""Returns the mass-weighted average velocity in cm/s.
+
+ This calculates and returns the mass-weighted average velocity of just
+ the particles in the halo in cm/s.
Examples
--------
@@ -463,6 +518,10 @@
def rms_velocity(self):
r"""Returns the mass-weighted RMS velocity for the halo
particles in cgs units.
+
+ Calculate and return the mass-weighted RMS velocity for just the
+ particles in the halo. The bulk velocity of the halo is subtracted
+ before computation.
Examples
--------
@@ -491,10 +550,13 @@
r"""Returns the maximum radius in the halo for all particles,
either from the point of maximum density or from the
center of mass.
+
+ The maximum radius from the most dense point is calculated. This
+ accounts for periodicity.
Parameters
- ---------
- center_of_mass : Boolean
+ ----------
+ center_of_mass : bool
True chooses the center of mass when calculating the maximum radius.
False chooses from the maximum density location for HOP halos
(it has no effect for FOF halos).
@@ -508,13 +570,14 @@
return self.max_radius
if center_of_mass: center = self.center_of_mass()
else: center = self.maximum_density_location()
+ DW = self.data.pf["DomainRightEdge"] - self.data.pf["DomainLeftEdge"]
if self.indices is not None:
rx = na.abs(self["particle_position_x"]-center[0])
ry = na.abs(self["particle_position_y"]-center[1])
rz = na.abs(self["particle_position_z"]-center[2])
- r = na.sqrt(na.minimum(rx, 1.0-rx)**2.0
- + na.minimum(ry, 1.0-ry)**2.0
- + na.minimum(rz, 1.0-rz)**2.0)
+ r = na.sqrt(na.minimum(rx, DW[0]-rx)**2.0
+ + na.minimum(ry, DW[1]-ry)**2.0
+ + na.minimum(rz, DW[2]-rz)**2.0)
my_max = r.max()
else:
@@ -539,17 +602,25 @@
def virial_mass(self, virial_overdensity=200., bins=300):
r"""Return the virial mass of the halo in Msun, using only the particles
- in the halo (no baryonic information used). Returns -1 if the halo is
- not virialized.
+ in the halo (no baryonic information used).
+
+ The virial mass is calculated, using the built in `Halo.virial_info`
+ functionality. The mass is then returned.
Parameters
----------
- virial_overdensity : Float
+ virial_overdensity : float
The overdensity threshold compared to the universal average when
calculating the virial mass. Default = 200.
- bins : Integer
+ bins : int
The number of spherical bins used to calculate overdensities.
Default = 300.
+
+ Returns
+ -------
+ mass : float
+ The virial mass in solar masses of the particles in the halo. -1
+ if not virialized.
Examples
--------
@@ -564,18 +635,26 @@
def virial_radius(self, virial_overdensity=200., bins=300):
- r"""Return the virial radius of the halo in code units, using only the
- particles in the halo (no baryonic information used). Returns -1 if the
- halo is not virialized.
+ r"""Return the virial radius of the halo in code units.
+
+ The virial radius of the halo is calculated, using only the particles
+ in the halo (no baryonic information used). Returns -1 if the halo is
+ not virialized.
Parameters
----------
- virial_overdensity : Float
+ virial_overdensity : float
The overdensity threshold compared to the universal average when
calculating the virial radius. Default = 200.
- bins : Integer
+ bins : integer
The number of spherical bins used to calculate overdensities.
Default = 300.
+
+ Returns
+ -------
+ radius : float
+ The virial raius in code units of the particles in the halo. -1
+ if not virialized.
Examples
--------
@@ -668,9 +747,11 @@
def center_of_mass(self):
r"""Calculate and return the center of mass.
+
+ The center of mass of the halo is directly calculated and returned.
Examples
- -------
+ --------
>>> com = halos[0].center_of_mass()
"""
pm = self["ParticleMassMsun"]
@@ -686,23 +767,11 @@
return com
def maximum_density(self):
- r"""Return the HOP-identified maximum density. Not applicable to
- FOF halos.
-
- Examples
- -------
- >>> max_dens = halos[0].maximum_density()
- """
+ r"""Not implemented."""
return -1
def maximum_density_location(self):
- r"""Return the location HOP identified as maximally dense. Not
- applicable to FOF halos.
-
- Examples
- -------
- >>> max_dens_loc = halos[0].maximum_density_location()
- """
+ r"""Not implemented."""
return self.center_of_mass()
class HaloList(object):
@@ -786,17 +855,19 @@
return self._groups[key]
def nearest_neighbors_3D(self, haloID, num_neighbors=7, search_radius=.2):
- r"""For a halo its nearest neighbors in 3D
- using the kd tree. Returns a list of the neighbors distances and ID
- with format [distance,haloID].
+ r"""For a halo its nearest neighbors in 3D using the kd tree.
+
+ This will calculate the nearest neighbors of a halo, using the kD tree.
+ Returns a list of the neighbors distances and ID with format
+ [distance,haloID].
Parameters
----------
- haloID : Integer
+ haloID : integer
The halo to find neighbors for.
- num_neighbors : Integer
+ num_neighbors : integer
How many neighbors to search for. Default = 7.
- search_radius : Float
+ search_radius : float
How far away to look for neighbors in code units. Default = 0.2.
Examples
@@ -829,19 +900,21 @@
def nearest_neighbors_2D(self, haloID, num_neighbors=7, search_radius=.2,
proj_dim=0):
- r"""For a halo its nearest neighbors in 2D
- using the kd tree. Returns a list of the neighbors distances and ID
- with format [distance,haloID].
+ r"""For a halo its nearest neighbors in 2D using the kd tree.
+
+ This will strip a dimension from consideration in the kD-tree, and then
+ calculate all the nearest projected neighbors of a halo. Returns a
+ list of the neighbors distances and ID with format [distance,haloID].
Parameters
----------
- haloID : Integer
+ haloID : int
The halo to find neighbors for.
- num_neighbors : Integer
+ num_neighbors : int
How many neighbors to search for. Default = 7.
- search_radius : Float
+ search_radius : float
How far away to look for neighbors in code units. Default = 0.2.
- proj_dim : Integer
+ proj_dim : int
Which dimension (0, 1, or 2) to project the halos into 2D.
Default = 0.
@@ -922,7 +995,7 @@
to a text file. Needed in particular for parallel analysis output.
Parameters
- ---------
+ ----------
prefix : String
The prefix for the name of the file.
@@ -1343,10 +1416,13 @@
def write_particle_lists_txt(self, prefix):
r"""Write out the names of the HDF5 files containing halo particle data
- to a text file. Needed in particular for parallel analysis output.
-
+ to a text file.
+
+ This function wirtes out the names of all the HDF5 files that would
+ contain halo particle data. Only the root processor writes out.
+
Parameters
- ---------
+ ----------
prefix : String
The prefix for the name of the file.
@@ -1360,6 +1436,13 @@
@parallel_blocking_call
def write_particle_lists(self, prefix):
r"""Write out the particle data for halos to HDF5 files.
+
+ This function will accept a filename prefix, and for every halo it will
+ write out an HDF5 file containing the positions, velocities, indices
+ and masses of the constituent particles. However, if the halo finder
+ is run in parallel, halos will only be written out on the processors to
+ which they belong. See `Halo.write_particle_lists_txt` for how to
+ track these halos globally across files.
Parameters
----------
@@ -1384,30 +1467,30 @@
Parameters
----------
pf : EnzoStaticOutput object
- threshold : Float
+ threshold : float
The density threshold used when building halos. Default = 160.0.
- dm_only : Boolean
+ dm_only : bool
If True, only dark matter particles are used when building halos.
Default = False.
- resize : Boolean
+ resize : bool
Turns load-balancing on or off. Default = True.
- rearrange : Boolean
+ rearrange : bool
Turns on faster nearest neighbor searches at the cost of increased
memory usage. Default = True.
- fancy_padding : Boolean
+ fancy_padding : bool
True calculates padding independently for each face of each
subvolume. Default = True.
- safety : Float
+ safety : float
Due to variances in inter-particle spacing in the volume, the
padding may need to be increased above the raw calculation.
This number is multiplied to the calculated padding, and values
>1 increase the padding. Default = 1.5.
- premerge : Boolean
+ premerge : bool
True merges chains in two steps (rather than one with False), which
can speed up halo finding by 25% or more. However, True can result
in small (<<1%) variations in the final halo masses when compared
to False. Default = True.
- sample : Float
+ sample : float
The fraction of the full dataset on which load-balancing is
performed. Default = 0.03.
@@ -1628,12 +1711,12 @@
Parameters
----------
pf : EnzoStaticOutput object
- threshold : Float
+ threshold : float
The density threshold used when building halos. Default = 160.0.
- dm_only : Boolean
+ dm_only : bool
If True, only dark matter particles are used when building halos.
Default = False.
- padding : Float
+ padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
must be no smaller than the radius of the largest halo in the box
@@ -1680,13 +1763,13 @@
Parameters
----------
pf : EnzoStaticOutput object
- link : Float
+ link : float
The interparticle distance (compared to the overall average)
used to build the halos. Default = 0.2.
- dm_only : Boolean
+ dm_only : bool
If True, only dark matter particles are used when building halos.
Default = False.
- padding : Float
+ padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
must be no smaller than the radius of the largest halo in the box
More information about the yt-svn
mailing list