#!/usr/bin/env python

#this script set up and runs several molecular dynamics trajectories
#this script must be called in the directory containing the n traj folders named as 000n
#a properly formatted Job file is required in the same foulder of the script

#################################################
from os import path, getcwd 			#
from os import chdir, system, mkdir		#
from time import sleep				#
from shutil import copy				#
#################################################

# Define calculation parameters #################
# this value will be used in the Job file #######
						#
#JobName			='D1elbow'	        # Just a general lable: "JobName_NumTraj"
TimeLimit               ='8'                    # in hours:             "TimeLimit:00:00"
Ntraj			=20000			#
Njobtraj		=1000			#
						#
#################################################
Njobs = int(Ntraj/Njobtraj)

here=getcwd()				#workdir

for i in range(Njobs):
	Nfirst = '%.6d' % (i*Njobtraj + 1)
	Nlast = '%.6d' % ( float(Nfirst) + Njobtraj - 1 )

	modify = 'sed -e \"s|_FIRSTJOB_|%s|g\" Job_mob_ > Job' % Nfirst 	# modify the Jobfile
	system(modify)								#
	modify = 'sed -i \"s|_TIMELIMIT_|%s|g\" Job' % TimeLimit                #
	system(modify)
	modify = 'sed -i \"s|_LASTJOB_|%s|g\" Job' % Nlast
	system(modify)

	system('qsub Job')	# RUN JOB #######################################
	sleep(1)