placed mergingThreshold parameter in defaults file

python_source/vide_pipeline/defaults.py

@@ -23,12 +23,23 @@ import os
 # -----------------------------------------------------------------------------
 # DEFAULT CONFIGURATION
 
+# the overall name for your dataset
 datasetName = ""
 
+# where to start and end the VIDE pipeline
+# stages:
+#   1 : extract redshift slices from data
+#   2 : void extraction using zobov
+#   3 : removal of small voids and voids near the edge
 startCatalogStage = 1
 endCatalogStage = 3
+
+# if True, will scan log files for last known completed state and run from there
 continueRun = True
 
+# re-build the inputs?
+regenerateFlag = False
+
 # directory for the input simulation/observational particle files
 catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
 
@@ -36,9 +47,9 @@ catalogDir = os.getenv("HOME")+"/workspace/Voids/catalog/"
 hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
 
 # where to put the final void catalog, figures, and output logs
-voidOutputDir = os.getenv("HOME")+"/workspace/Voids//"
-figDir = os.getenv("PWD")+"/../figs/"
-logDir = os.getenv("PWD")+"/../logs/"
+workDir = os.getenv("PWD")+"/output/"
+figDir = os.getenv("PWD")+"/figs/"
+logDir = os.getenv("PWD")+"/logs/"
 
 # where to place the pipeline scripts
 scriptDir = os.getenv("PWD")+"/scripts//"
@@ -127,6 +138,11 @@ haloFilePosRescale = 1.0 # rescaling necessary to get Mpc/h
 numZobovDivisions = 2
 numZobovThreads = 2
 
+# Maximum density for merging voids
+#   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
+#   1e-9 (or smaller != 0) -> Do not merge anything
+mergingThreshold = 1.e-9
+
 # simulation information
 numPart = 512*512*512
 lbox = 999.983 # Mpc/h