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

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

scripts/density_area.py

@@ -0,0 +1,97 @@
+#!/usr/bin/python 
+
+# Script:  density_area.py
+# Purpose: binned atom density by atom type and running area under the curve
+# Syntax:  density.py x/y/z nbin outfile files ...
+#          x/y/z = get density distribution along this axis
+#          nbin = # of bins in desired direction
+#          outfile = file to write flux stats to
+#          files = series of dump files
+# Example: density_area.py z 100 dens.out dump.*
+# Author:  Paul Crozier (Sandia).
+#          Modified by Jeff Greathouse (Sandia) to include
+#          calculation of area under the curve
+
+# enable script to run from Python directly w/out Pizza.py
+
+import sys
+from dump import dump
+if not globals().has_key("argv"): argv = sys.argv
+
+# main script
+
+if len(argv) < 5:
+  raise StandardError, "Syntax: density.py x/y/z nbin outfile files ..."
+
+direction = argv[1]
+nbins = int(argv[2])
+outfile = argv[3]
+files = ' '.join(argv[4:])
+
+# read snapshots one-at-a-time
+
+d = dump(files,0)
+d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
+
+first = 1
+nsnaps = 0
+ntypes = 0
+while 1:
+  time = d.next()
+  if time == -1: break
+
+  if first:
+    tmp,ntypes = d.minmax("type")
+    ntypes = int(ntypes)
+    bin = nbins * [0]
+    for i in xrange(nbins): bin[i] = ntypes * [0]
+    first = 0
+    
+  box = (d.snaps[-1].xlo,d.snaps[-1].ylo,d.snaps[-1].zlo,
+         d.snaps[-1].xhi,d.snaps[-1].yhi,d.snaps[-1].zhi)
+  vol = (box[3] - box[0]) * (box[4] - box[1]) * (box[5] - box[2]) 
+
+  if direction == "x": type,x = d.vecs(time,"type","x")
+  elif direction == "y": type,x = d.vecs(time,"type","y")
+  elif direction == "z": type,x = d.vecs(time,"type","z")
+  
+  type = map(int,type)
+  natoms = len(type)
+  for i in xrange(natoms): type[i] -= 1
+  
+  for i in xrange(natoms):
+    ibin = int(nbins*x[i] + 0.5)
+    if (ibin < 0): ibin += nbins
+    if (ibin > nbins-1): ibin -= nbins
+    bin[ibin][type[i]] += nbins/vol
+  nsnaps += 1
+  print time,
+  
+print
+print "Printing ",direction,"-directional density distribution in mol/L to", \
+      outfile
+conversion = 1660.53873              # convert from atoms/Angs^3 to mol/L
+    
+# Output as x, density_1, area_1, ...
+
+fp = open(outfile,"w")
+first = 1
+xden = nbins * [0]
+yden = nbins * [0]
+for i in xrange(nbins): yden[i] = ntypes * [0]
+sum = ntypes * [0]
+for i in xrange(nbins):
+  xden[i] = float(i)/float(nbins)
+  print >>fp, xden[i],
+  if first:
+    for j in xrange(ntypes):
+      yden[i][j] = conversion*bin[i][j]/nsnaps
+      print >>fp, yden[i][j], sum[j],
+    first = 0
+  else:
+    for j in xrange(ntypes):
+      yden[i][j] = conversion*bin[i][j]/nsnaps
+      sum[j] += 0.5 * (xden[i] - xden[i-1]) * (yden[i][j] + yden[i-1][j])
+      print >>fp, yden[i][j], sum[j],
+  print >>fp 
+fp.close()