#!/usr/bin/env python
import sys, commands
from os import path, getcwd
from os import chdir, system, mkdir
from shutil import copy
import numpy as np

first = 1
last = 500

# Define calculation parameters #################
# this value will be used in the Job file #######
						#
JobName			='163v1_ET'	# Just a general lable: "JobName_NumTraj"
TimeLimit		='1'			# in hours:		"TimeLimit:00:00"
NCores			='24'			#
						#
#################################################

here=getcwd()				#workdir
for i in range(first,(last+1)):
	traj= '%.4d' % i		# define working directory
	newdir=path.join(here, traj)	# updating mypath

	if not path.exists(newdir): 
		print "folder", newdir, "not found. exiting..."
		quit()

	chdir(newdir)	

	if not path.exists('EnergyTransfer'):
		mkdir('EnergyTransfer')

	if path.exists('EnergyTransfer/OSZICAR_initial') and path.exists('EnergyTransfer/OSZICAR_final'):
		continue

	chdir('EnergyTransfer')

	Initial_conf = open('POSCAR_initial', 'w')
	Final_conf = open('POSCAR_final', 'w')

	### Initial
	POSCAR = open('../POSCAR_1').readlines()

	### Header
	Initial_conf.write("C O H\n")
	for i in range(1, 5):
		Initial_conf.write(POSCAR[i])
	Initial_conf.write("C O H\n")
	Initial_conf.write("1 1 4\n")
	for i in range(7, 9):
		Initial_conf.write(POSCAR[i])

	### POSCAR - Methane
	for i in range(57, 63):
		Initial_conf.write(POSCAR[i][0:-7])
		Initial_conf.write("   T   T   T\n")

	Initial_conf.write('\n')

	for i in range(112, 118):
		Initial_conf.write(POSCAR[i])

	### Final
	check = 1
	while path.exists('../CONTCAR_' + str(check)):
		check += 1
	check -= 1
	CONTCAR = open('../CONTCAR_' + str(check)).readlines()

	### Header
	Final_conf.write("C O H\n")
	for i in range(1, 5):
		Final_conf.write(CONTCAR[i])
	Final_conf.write("C O H\n")
	Final_conf.write("1 1 4\n")
	for i in range(7, 9):
		Final_conf.write(CONTCAR[i])

	### POSCAR - Methane
	for i in range(57, 63):
		Final_conf.write(CONTCAR[i][0:-13])
		Final_conf.write("   T   T   T\n")

	Final_conf.write('\n')

	for i in range(112, 118):
		Final_conf.write(CONTCAR[i])

	if not path.exists('Job-ET'):	# otherwise the calculation has already been started sometimes

		copy('%s/INPUTS/Job-ET'		% here	, 'Job-ET')			#
		system('cp %s/INPUTS/ET_INCAR INCAR'		% here )				#
		system('cp %s/INPUTS/POTCAR_methanol POTCAR'		% here )
		system('cp %s/INPUTS/KPOINTS .'		% here )
		system('cp %s/INPUTS/vdw_kernel.bindat .'		% here )

		lable = traj + '_' + JobName							
		modify = 'sed -e \"s|_JOBNAME_|%s|g\" Job-ET > Job' % lable 		# modify the Jobfile
		system(modify)								#
		modify = 'sed -i \"s|_TIMELIMIT_|%s|g\" Job' % TimeLimit		#
		system(modify)								#
		modify = 'sed -i \"s|_NCORES_|%s|g\" Job' % NCores			#
	       	system(modify)								#

		system('sbatch Job > ID.job')	# RUN JOB #######################################
		system('cat ID.job')