# HG changeset patch
# User Stephen Skory <stephenskory@yahoo.com>
# Date 1247000605 25200
# Branch hopwrap
# Node ID 9b51d2a3582605f24d11399df7882f5ccc2c172b
# Parent  19aa8984a3d3590f0bfc44a7d599c1e0b75d9cbb
A few more bugs in chainHOP.

diff -r 19aa8984a3d3590f0bfc44a7d599c1e0b75d9cbb -r 9b51d2a3582605f24d11399df7882f5ccc2c172b yt/extensions/kdtree/fKD_source.f90
--- a/yt/extensions/kdtree/fKD_source.f90	Mon Jul 06 17:18:49 2009 -0700
+++ b/yt/extensions/kdtree/fKD_source.f90	Tue Jul 07 14:03:25 2009 -0700
@@ -1115,7 +1115,7 @@
   end subroutine kdtree2_n_nearest_around_point
 
   subroutine kdtree2_r_nearest(tp,qv,r2,nfound,nalloc,results) 
-    ! find the nearest neighbors to point 'idxin', within SQUARED
+    ! find the nearest neighbors to point 'qv', within SQUARED
     ! Euclidean distance 'r2'.   Upon ENTRY, nalloc must be the
     ! size of memory allocated for results(1:nalloc).  Upon
     ! EXIT, nfound is the number actually found within the ball. 
diff -r 19aa8984a3d3590f0bfc44a7d599c1e0b75d9cbb -r 9b51d2a3582605f24d11399df7882f5ccc2c172b yt/lagos/HaloFinding.py
--- a/yt/lagos/HaloFinding.py	Mon Jul 06 17:18:49 2009 -0700
+++ b/yt/lagos/HaloFinding.py	Tue Jul 07 14:03:25 2009 -0700
@@ -605,10 +605,10 @@
             halo.write_particle_list(f)
 
 class chainHF(GenericHaloFinder, chainHOPHaloList):
-    def __init__(self, pf, threshold=160, dm_only=True, num_neighbors=64):
+    def __init__(self, pf, threshold=160, dm_only=True):
         GenericHaloFinder.__init__(self, pf, dm_only, padding=0.0)
         self.padding = 0.0 
-        self.num_neighbors = num_neighbors
+        self.num_neighbors = 65
         # get the total number of particles across all procs, with no padding
         padded, LE, RE, self._data_source = self._partition_hierarchy_3d(padding=self.padding)
         # also get the total mass of particles
diff -r 19aa8984a3d3590f0bfc44a7d599c1e0b75d9cbb -r 9b51d2a3582605f24d11399df7882f5ccc2c172b yt/lagos/chainHOP/chainHOP.py
--- a/yt/lagos/chainHOP/chainHOP.py	Mon Jul 06 17:18:49 2009 -0700
+++ b/yt/lagos/chainHOP/chainHOP.py	Tue Jul 07 14:03:25 2009 -0700
@@ -43,7 +43,7 @@
         fKD.qv = empty(3,dtype='d')
         fKD.nn = self.num_neighbors
         fKD.nparts = size
-        fKD.sort = False # faster, but unordered neighbors (OK for chainHOP)
+        fKD.sort = True # slower, but needed in _connect_chains
         fKD.rearrange = True # faster, more memory
         # this actually copies the data into the fortran space
         fKD.pos[0,:] = self.xpos
@@ -146,7 +146,8 @@
             # if this particle is in the padding, don't make a connection
             if part.is_inside is False: continue
             # loop over nearest neighbors
-            for i in range(self.num_neighbors):
+            #for i in range(self.num_neighbors):
+            for i in range(self.nMerge+2):
                 thisNN = part.NNtags[i]
                 # if our neighbor is in the same chain, move on
                 if part.chainID == self.NN[thisNN].chainID: continue
@@ -197,7 +198,7 @@
                     #print 'neither already assigned'
                     groupID += 1
         # chains that haven't been linked to another chain increase the count
-        # by themselves and change label
+        # by themselves and change label. Also add to chain_connections
         for i in range(chain_count):
             if self.reverse_map[i] == -1:
                 self.reverse_map[i] = groupID
@@ -281,6 +282,7 @@
 
     def _chainHOP(self):
         size = len(self.xpos)
+        self.nMerge = 4
         mylog.info('Building kd tree for %d particles...' % \
             size)
         self.__init_kd_tree(size)