Committer: ckloss <ckloss@fluid38.(none)>

On branch master
 Initial commit for lpp, version 2011-10-11

scripts/cluster.py

@@ -0,0 +1,123 @@
+#!/usr/bin/python
+
+# Script:  cluster.py
+# Purpose: histogram of cluster size of type2 atoms near type1
+# Syntax:  cluster.py type1 type2 cutoff nbin dump.1 dump.2 ...
+#          type1,type2 = atom types (1-N)
+#          cutoff = only consider atom pairs within distance cutoff
+#          nbin = # of bins for histogram
+#          files = series of dump files
+# Example: cluster.py 1 5 2.0 10 dump.*
+# Author:  Steve Plimpton (Sandia)
+
+# for all snapshots, for each type1 atom, count # of type2 atoms within cutoff
+# will be very slow (N^2) if are too many type1 atoms
+
+# enable script to run from Python directly w/out Pizza.py
+
+import sys
+from dump import dump
+from gnu import gnu
+if not globals().has_key("argv"): argv = sys.argv
+
+# main script
+
+# function to compute distance sq between 2 atoms with PBC
+
+def distance(atom1,atom2,box):
+  x1 = atom1[2]
+  y1 = atom1[3]
+  z1 = atom1[4]
+  x2 = atom2[2]
+  y2 = atom2[3]
+  z2 = atom2[4]
+  
+  delx = x2 - x1
+  dely = y2 - y1
+  delz = z2 - z1
+  
+  xprd = box[3] - box[0]
+  yprd = box[4] - box[1]
+  zprd = box[5] - box[2]
+
+  if abs(delx) > 0.5*xprd:
+    if delx < 0.0:
+      delx += xprd
+    else:
+      delx -= xprd
+  if abs(dely) > 0.5*yprd:
+    if dely < 0.0:
+      dely += yprd
+    else:
+      dely -= yprd
+  if abs(delz) > 0.5*zprd:
+    if delz < 0.0:
+      delz += zprd
+    else:
+      delz -= zprd
+      
+  distsq = delx*delx + dely*dely + delz*delz
+  return distsq
+
+# main script
+
+if len(argv) < 6:
+  raise StandardError,"cluster.py type1 type2 cutoff nbin dump.1 dump.2 ..."
+
+type1 = int(argv[1])
+type2 = int(argv[2])
+cutoff = float(argv[3])
+nbin = int(argv[4])
+files = ' '.join(argv[5:])
+
+# read in dump file(s) and select only type1 or type2 atoms
+
+d = dump(files)
+d.aselect.test("$type == %d or $type == %d" % (type1,type2))
+
+# loop over snapshots
+# viz returns list of atoms in one snapshot
+
+cutsq = cutoff*cutoff
+cluster = nbin*[0]
+
+print "Clustering ..."
+
+flag = 0
+while 1:
+  which,time,flag = d.iterator(flag)
+  if flag == -1: break
+  time,box,atoms,bonds,tris = d.viz(which)
+  print time,
+  sys.stdout.flush()
+
+  # loop over all type1 atoms
+  
+  n = len(atoms)
+  for i in xrange(n):
+    itype = atoms[i][1]
+    if itype != type1: continue
+    ncount = 0
+
+    # loop over all type2 atoms
+    # increment cluster count if distance is within cutoff
+    
+    for j in xrange(n):
+      jtype = atoms[j][1]
+      if jtype != type2 or i == j: continue 
+      distsq = distance(atoms[i],atoms[j],box)
+      if distsq < cutsq: ncount += 1
+
+    # increment histogram count
+    
+    if ncount >= nbin: cluster[nbin-1] += 1
+    else: cluster[ncount] += 1
+
+print
+print "Cluster size and count:"
+for i in range(nbin): print i,cluster[i]
+
+# comment out if don't want plot
+
+#g = gnu()
+#g.plot(range(nbin),cluster)