forked from lijiext/lammps
37 lines
906 B
Python
Executable File
37 lines
906 B
Python
Executable File
#!/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
|