#!/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               ='1'                    # in hours:             "TimeLimit:00:00"
Ntraj			=1			#
Njobtraj		=1			#
Name			='54-323K-RPMD'
						#
#################################################
if (Ntraj % Njobtraj) != 0.:
	print('WARNING: Ntraj/Njobtraj is not an integer')
	exit()
Njobs = int(Ntraj/Njobtraj)

here=getcwd()				#workdir

for i in range(Njobs):
	Nfirst = '{:06d}'.format( i*Njobtraj )
	Nlast = '{:06d}'.format( int(Nfirst) + Njobtraj - 1 )

	modify = 'sed -e \"s|_FIRSTJOB_|{:s}|g\" Job_ > Job'.format( Nfirst )
	system(modify)								#
	modify = 'sed -i \"s|_TIMELIMIT_|{:s}|g\" Job'.format( TimeLimit )
	system(modify)
	modify = 'sed -i \"s|_LASTJOB_|{:s}|g\" Job'.format( Nlast )
	system(modify)
	modify = 'sed -i \"s|_NAME_|{:s}|g\" Job'.format( Name )
	system(modify)

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