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

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

scripts/density2d.py

@@ -0,0 +1,138 @@
+#!/usr/bin/python 
+
+# Script:    density2d.py
+# Purpose:   binned atom density by atom type
+# Syntax:    density.py x/y/z nbin vmin vmax outfile files ...
+#            x/y/z = get density distribution along this (vertical) axis,
+#                    bining along the other two (planar) axes
+#            nbin = # of bins along each of planar axes
+#            vmin, vmax = min and max along the vertical axis,
+#                    use 0 for both for the complete box
+#            outfile = file to write flux stats to
+#            files = series of dump files
+# Example: density2d.py z 100 dens.out dump.*
+# Modified from density.py:  David Hart (Sandia)
+
+# enable script to run from Python directly w/out Pizza.py
+
+import sys
+import numpy as np
+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 vmin vmax outfile files ..."
+
+direction = argv[1]
+nbins = int(argv[2])
+if nbins < 1:
+    nbins = 100
+try:
+    zmin = float(argv[3])
+except ValueError:
+    zmin = -np.inf
+try:
+    zmax = float(argv[4])
+except ValueError:
+    zmax = np.inf
+if zmax == zmin:
+    zmin = -np.inf
+    zmax = np.inf
+outfile = argv[5]
+files = ' '.join(argv[6:])
+
+# read snapshots one-at-a-time
+
+d = dump(files,0)
+d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
+bidirect = 'x/y'
+first = 1
+nsnaps = 0
+dx = 0
+dy = 0
+x0 = 0
+y0 = 0
+vol = 0
+
+while 1:
+    time = d.next()
+    if time == -1: break
+
+    if first:
+        tmp,ntypes = d.minmax("type")
+        ntypes = int(ntypes)
+        bin = np.zeros(shape=(nbins,nbins,ntypes))
+        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 == "z": 
+        type,x,y,z = d.vecs(time,"type","x","y","z")
+        bidirect = 'x/y'
+        dx = box[3] - box[0]
+        dy = box[4] - box[1]
+        dz = box[5] - box[2]
+        x0 = box[0] + float(dx)/float(nbins)/2.0
+        y0 = box[1] + float(dy)/float(nbins)/2.0
+        zmax = min(zmax,box[5])
+        zmin = max(zmin,box[2])
+    elif direction == "y":
+        type,x,y,z = d.vecs(time,"type","x","z","y")
+        bidirect = 'x/z'
+        dx = box[3] - box[0]
+        dy = box[5] - box[2]
+        dz = box[4] - box[1]
+        x0 = box[0] + float(dx)/float(nbins)/2.0
+        y0 = box[2] + float(dy)/float(nbins)/2.0
+        zmax = min(zmax,box[4])
+        zmin = max(zmin,box[1])
+    elif direction == "x": 
+        type,x,y,z = d.vecs(time,"type","y","z","x")
+        bidirect = 'y/z'
+        dx = box[4] - box[1]
+        dy = box[5] - box[2]
+        dz = box[3] - box[0]
+        x0 = box[1] + float(dx)/float(nbins)/2.0
+        y0 = box[2] + float(dy)/float(nbins)/2.0
+        zmax = min(zmax,box[3])
+        zmin = max(zmin,box[0])
+    vol = dx * dy * float(zmax - zmin)
+
+    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])
+        jbin = int(nbins*y[i])
+        zloc = float(z[i])*float(dz)
+        if zloc < zmin or zloc > zmax: continue
+        if (ibin < 0): ibin = 0
+        if (ibin > nbins-1): ibin = nbins - 1
+        if (jbin < 0): jbin = 0
+        if (jbin > nbins-1): jbin = nbins - 1
+        bin[jbin][ibin][type[i]] += nbins*nbins/vol
+    nsnaps += 1
+    print time,
+
+print 
+print "Printing %s-mapped density distribution for %s-slice [%.2f,%.2f] in mol/L to %s" %(bidirect, direction, zmin, zmax, outfile)
+conversion = 1660.53873  # convert from atoms/Angs^3 to mol/L
+        
+fp = open(outfile,"w")
+# '''Uncomment for column headers. Commented for consistency with density.py'''
+# print >>fp, " %8s  %8s " %('ra', 'rb'),
+# for k in xrange(ntypes):
+#     print >>fp, " %8s " %(k),
+# print >>fp
+for i in xrange(nbins):
+    for j in xrange(nbins):
+        print >>fp, " %8.3f  %8.3f " %(float(i)/float(nbins)*float(dx)+float(x0), float(j)/float(nbins)*float(dy)+float(y0)),
+        for k in xrange(ntypes):
+            print >>fp, " %8.3f " % (conversion*bin[j][i][k]/nsnaps),
+        print >>fp 
+fp.close()