[Yt-svn] yt: 1. Bug fixes and upgrades to the StarAnalysis stuff.

[hg at spacepope.org]

hg Repository: yt
details:   yt/rev/4f3965faa48c
changeset: 1465:4f3965faa48c
user:      Stephen Skory <stephenskory at yahoo.com>
date:
Sun Mar 21 16:18:08 2010 -0700
description:
1. Bug fixes and upgrades to the StarAnalysis stuff.
2. The python-native kd tree really sucks. I've effectively turned it
into a brute-force search with this change. But for some reason it
isn't finding the correct nearest neighbors. I think slow but correct
is preferable to fast(ish) and wrong.
3. Small changes to the parallel HOP code for mpi_get_size/rank().

diffstat:

 yt/extensions/StarAnalysis.py       |  15 ++++++++++++---
 yt/lagos/HaloFinding.py             |   4 ++--
 yt/lagos/kd.py                      |   2 +-
 yt/lagos/parallelHOP/parallelHOP.py |   5 +----
 4 files changed, 16 insertions(+), 10 deletions(-)

diffs (102 lines):

diff -r 1aa6eb842a66 -r 4f3965faa48c yt/extensions/StarAnalysis.py
--- a/yt/extensions/StarAnalysis.py	Sun Mar 21 14:58:21 2010 -0700
+++ b/yt/extensions/StarAnalysis.py	Sun Mar 21 16:18:08 2010 -0700
@@ -215,7 +215,7 @@
     
     def calculate_spectrum(self, data_source=None, star_mass=None,
             star_creation_time=None, star_metallicity_fraction=None,
-            star_metallicity_constant=None):
+            star_metallicity_constant=None, min_age=0.):
         """
         For the set of stars, calculate the collective spectrum.
         Attached to the output are several useful objects:
@@ -233,6 +233,8 @@
         metallicity fractions, in code units (which is not Z/Zsun).
         :param star_metallicity_constant (float): If desired, override the star
         metallicity fraction of all the stars to the given value.
+        :param min_age (float): Removes young stars below this number (in years
+        from the spectrum. Default: 0 (all stars).
         """
         # Initialize values
         self.final_spec = na.zeros(self.wavelength.size, dtype='float64')
@@ -240,6 +242,7 @@
         self.star_mass = star_mass
         self.star_creation_time = star_creation_time
         self.star_metal = star_metallicity_fraction
+        self.min_age = min_age
         
         # Check to make sure we have the right set of data.
         if data_source is None:
@@ -273,8 +276,13 @@
         self.star_metal /= Zsun
         # Age of star in years.
         dt = (self.time_now - self.star_creation_time * self._pf['Time']) / YEAR
+        # Remove young stars
+        sub = dt > self.min_age
+        self.star_metal = self.star_metal[sub]
+        dt = dt[sub]
+        self.star_creation_time = self.star_creation_time[sub]
         # Figure out which METALS bin the star goes into.
-        Mindex = na.digitize(dt, METALS)
+        Mindex = na.digitize(self.star_metal, METALS)
         # Replace the indices with strings.
         Mname = MtoD[Mindex]
         # Figure out which age bin this star goes into.
@@ -284,7 +292,8 @@
         ratio2 = (self.age[Aindex] - dt) / (self.age[Aindex] - self.age[Aindex-1])
         # Sort the stars by metallicity and then by age, which should reduce
         # memory access time by a little bit in the loop.
-        sort = na.lexsort((Aindex, Mname))
+        indexes = na.arange(self.star_metal.size)
+        sort = na.asarray([indexes[i] for i in na.lexsort([indexes, Aindex, Mname])])
         Mname = Mname[sort]
         Aindex = Aindex[sort]
         ratio1 = ratio1[sort]
diff -r 1aa6eb842a66 -r 4f3965faa48c yt/lagos/HaloFinding.py
--- a/yt/lagos/HaloFinding.py	Sun Mar 21 14:58:21 2010 -0700
+++ b/yt/lagos/HaloFinding.py	Sun Mar 21 16:18:08 2010 -0700
@@ -1144,7 +1144,7 @@
         # Adaptive subregions by bisection.
         ds_names = ["particle_position_x","particle_position_y","particle_position_z"]
         if ytcfg.getboolean("yt","inline") == False and \
-           resize and self._mpi_get_size() is not None:
+           resize and self._mpi_get_size() != 1:
             cut_list = self._partition_hierarchy_3d_bisection_list()
             for i,cut in enumerate(cut_list):
                 dim = cut[0]
@@ -1180,7 +1180,7 @@
             del bins, counts
         # If this isn't parallel, define the region as an AMRRegionStrict so
         # particle IO works.
-        if self._mpi_get_size() == None or self._mpi_get_size() == 1:
+        if self._mpi_get_size() == 1:
             self._data_source = self.hierarchy.periodic_region_strict([0.5]*3, LE, RE)
         # get the average spacing between particles for this region
         # The except is for the serial case, where the full box is what we want.
diff -r 1aa6eb842a66 -r 4f3965faa48c yt/lagos/kd.py
--- a/yt/lagos/kd.py	Sun Mar 21 14:58:21 2010 -0700
+++ b/yt/lagos/kd.py	Sun Mar 21 16:18:08 2010 -0700
@@ -223,7 +223,7 @@
     
     # if this node is close enough (the distances are calculated in the previous
     # iteration), or if the query point is inside the node, continue on
-    if (neighbors.minDistanceSquared > distanceSquared) or inside:
+    if True or inside:
         # leafs don't have children, so this tests to see if this node
         # is a leaf, and if it is a leaf, calculate distances to the query point
         if (node.leftChild is None):
diff -r 1aa6eb842a66 -r 4f3965faa48c yt/lagos/parallelHOP/parallelHOP.py
--- a/yt/lagos/parallelHOP/parallelHOP.py	Sun Mar 21 14:58:21 2010 -0700
+++ b/yt/lagos/parallelHOP/parallelHOP.py	Sun Mar 21 16:18:08 2010 -0700
@@ -1131,10 +1131,7 @@
         Set_list = []
         # We only want the holes that are modulo mine.
         keys = na.arange(groupID, dtype='int64')
-        if self._mpi_get_size() == None:
-            size = 1
-        else:
-            size = self._mpi_get_size()
+        size = self._mpi_get_size()
         select = (keys % size == self.mine)
         groupIDs = keys[select]
         mine_groupIDs = set([]) # Records only ones modulo mine.