git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11955 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/fep/fdti.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+# fdti.py - integrate compute fep results using the trapezoidal rule
+
+import sys, math
+
+if len(sys.argv) < 3:
+    print "Finite Difference Thermodynamic Integration (Mezei 1987)"
+    print "Trapezoidal integration of compute_fep results at equally-spaced points"
+    print "usage: fdti.py temperature hderiv < fep.lmp"
+    sys.exit()
+
+rt = 0.008314 / 4.184 * float(sys.argv[1])
+hderiv = float(sys.argv[2])
+
+line = sys.stdin.readline()
+while line.startswith("#"):
+    line = sys.stdin.readline()
+
+v = 1.0
+tok = line.split()
+if len(tok) == 4:
+    v = float(tok[3])
+lo = -rt * math.log(float(tok[2]) / v)
+    
+i = 0
+sum = 0.0
+for line in sys.stdin:
+    tok = line.split()
+    if len(tok) == 4:
+        v = float(tok[3])
+    hi = - rt * math.log(float(tok[2]) / v)
+    sum += (hi + lo) / (2 * hderiv)
+    lo = hi
+    i += 1
+
+print sum / i      # int_0^1: divide by i == multiply by delta