fdti.py
739b14fae00fefficient_neuronet

fdti.py
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			#!/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