[Yt-svn] yt-commit r1563 - in trunk/yt: . lagos lagos/parallelHOP

[sskory at wrangler.dreamhost.com]

Author: sskory
Date: Mon Dec 21 10:32:30 2009
New Revision: 1563
URL: http://yt.enzotools.org/changeset/1563

Log:
Adding my premerge parameter for parallel HOP

Modified:
   trunk/yt/lagos/HaloFinding.py
   trunk/yt/lagos/parallelHOP/parallelHOP.py
   trunk/yt/mods.py

Modified: trunk/yt/lagos/HaloFinding.py
==============================================================================
--- trunk/yt/lagos/HaloFinding.py	(original)
+++ trunk/yt/lagos/HaloFinding.py	Mon Dec 21 10:32:30 2009
@@ -793,7 +793,7 @@
               ["ParticleMassMsun", "particle_index"]
 
     def __init__(self, data_source, padding, num_neighbors, bounds, total_mass,
-        period, threshold=160.0, dm_only=True, rearrange=True):
+        period, threshold=160.0, dm_only=True, rearrange=True, premerge=True):
         """
         Run hop on *data_source* with a given density *threshold*.  If
         *dm_only* is set, only run it on the dark matter particles, otherwise
@@ -806,6 +806,7 @@
         self.rearrange = rearrange
         self.period = period
         self._data_source = data_source
+        self.premerge = premerge
         mylog.info("Initializing HOP")
         HaloList.__init__(self, data_source, dm_only)
 
@@ -828,7 +829,7 @@
             self.particle_fields["particle_position_z"],
             self.particle_fields["particle_index"],
             self.particle_fields["ParticleMassMsun"]/self.total_mass,
-            self.threshold, rearrange=self.rearrange)
+            self.threshold, rearrange=self.rearrange, premerge=self.premerge)
         self.densities, self.tags = obj.density, obj.chainID
         # I'm going to go ahead and delete self.densities because it's not
         # actually being used. I'm not going to remove it altogether because
@@ -1056,7 +1057,7 @@
 
 class parallelHF(GenericHaloFinder, parallelHOPHaloList):
     def __init__(self, pf, threshold=160, dm_only=True, resize=True, rearrange=True,\
-        fancy_padding=True, safety=1.5):
+        fancy_padding=True, safety=1.5, premerge=True):
         GenericHaloFinder.__init__(self, pf, dm_only, padding=0.0)
         self.padding = 0.0 
         self.num_neighbors = 65
@@ -1177,7 +1178,7 @@
         (LE_padding, RE_padding) = self.padding
         parallelHOPHaloList.__init__(self, self._data_source, self.padding, \
         self.num_neighbors, self.bounds, total_mass, period, \
-        threshold=threshold, dm_only=dm_only, rearrange=rearrange)
+        threshold=threshold, dm_only=dm_only, rearrange=rearrange, premerge=premerge)
         self._join_halolists()
         yt_counters("Final Grouping")
 

Modified: trunk/yt/lagos/parallelHOP/parallelHOP.py
==============================================================================
--- trunk/yt/lagos/parallelHOP/parallelHOP.py	(original)
+++ trunk/yt/lagos/parallelHOP/parallelHOP.py	Mon Dec 21 10:32:30 2009
@@ -33,9 +33,11 @@
 
 class RunParallelHOP(ParallelAnalysisInterface):
     def __init__(self,period, padding, num_neighbors, bounds,
-            xpos, ypos, zpos, index, mass, threshold=160.0, rearrange=True):
+            xpos, ypos, zpos, index, mass, threshold=160.0, rearrange=True,
+            premerge=True):
         self.threshold = threshold
         self.rearrange = rearrange
+        self.premerge = premerge
         self.saddlethresh = 2.5 * threshold
         self.peakthresh = 3 * threshold
         self.period = period
@@ -1417,7 +1419,8 @@
         # This array tracks whether or not relationships for this particle
         # need to be examined twice, in preconnect_chains and in connect_chains
         self.search_again = na.ones(self.size, dtype='bool')
-        chain_count = self._preconnect_chains(chain_count)
+        if self.premerge:
+            chain_count = self._preconnect_chains(chain_count)
         mylog.info('Gobally assigning chainIDs...')
         self._globally_assign_chainIDs(chain_count)
         mylog.info('Globally finding densest in chains...')

Modified: trunk/yt/mods.py
==============================================================================
--- trunk/yt/mods.py	(original)
+++ trunk/yt/mods.py	Mon Dec 21 10:32:30 2009
@@ -43,7 +43,7 @@
     derived_field, \
     add_field, FieldInfo, EnzoFieldInfo, Enzo2DFieldInfo, OrionFieldInfo, \
     Clump, write_clump_hierarchy, find_clumps, write_clumps, \
-    OrionStaticOutput, HaloFinder, HOPHaloFinder, FOFHaloFinder, \
+    OrionStaticOutput, HaloFinder, HOPHaloFinder, FOFHaloFinder, parallelHF, \
     axis_names, x_dict, y_dict
 
 # This is a temporary solution -- in the future, we will allow the user to