#!/bin/env python
# calculate new replica exchange temperature according to the old temperature and exchange rate
import sys, re
from lnx_util import parseInput, print_help
import subprocess
inputP= parseInput(sys.argv[1:])
paraOpt = '-flog -h'.split()
helpdoc=\
'''
Usage! ./prog.py
-flog run1_0.log ; log file from any replica
-h ; print help information
'''
print_help(inputP, paraOpt, helpdoc)
finm = inputP['-flog']
rate = 0.25
exe = 'grep \'Repl fake T\' run1_0.log '
p= subprocess.Popen( exe, shell=True, stdout=subprocess.PIPE)
temperature = [ float(i) for i in re.findall('\d*\.*\d*', p.stdout.readline() ) if len(i) >0 ]
exe = 'grep -A 2 \'Repl average probabilities:\' run1_0.log | tail -n 1 '
p= subprocess.Popen( exe, shell=True, stdout=subprocess.PIPE)
# main file to modify topology for rest
import sys
import rest_lipid_top, rest_force_field_top
import lnx_util
inputP = lnx_util.parseInput(sys.argv[1:])
paraOpt = "-top -bondedTop -nonbondedTop -otop -obonded -ononbonded -T1 -T2 -sep -h".split()
helpdoc = (
"Usage! ./prog.py \n"
" -top top1 ; topology file for solutes that need rescale\n"
" -bondedTop top2 ; force field file that contains bonded and non_boned interactions\n"
" -nonbondedTop top3 ;\n"
" -otop outTop1 ; topology modified from top1\n"
" -obonded outTopbonded ; topology modified for bonded\n"
" -ononbonded outTopnonbonded ; topology modified for nonbonded\n"
" -T1 323 k ; \n"
" -T2 600 k ; gamma = beta_2 / beta_1 \n"
" ; charge: q_i = sqrt(gamma) *q_i ;\n"
" ; vdw : epsilon_i = epsilon_i * gamma ; i belongs to solute ;\n"
" -sep ; when sep flag is set, we print the topology as an individual top rather than free energy format \n"
" -h ; print help doc \n"
)
lnx_util.print_help(inputP, paraOpt, helpdoc)
t1 = float(inputP["-T1"])
t2 = float(inputP["-T2"])
gamma = t1 / t2
print "gamma: %5.3f" % gamma