W2RC_ref

#!/bin/bash
#    Copyright (C) 2013 Thomas Carette


if [ ! -e $1 ]
then
  echo "$1 do not exists"
  exit
fi

nl='
'

if [ "$4" == 'Ne' ]
then
  actc="2${nl}2${nl}6${nl}"
  orb="3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 5g 6s 6p 6d 6f 6g 6h 7s 7p 7d 7f 7g 7h 7i 8s 8p 8d 8f 8g 8h 8i 8k 9s 9p 9d 9f 9g 9h 9i 9k 9l :s :p :d :f :g :h :i :k :l :m ;s ;p ;d ;f ;g ;h ;i ;k ;l ;m ;n <s <p <d <f <g <h <i <k <l <m <n =s =p =d =f =g =h =i =k =l =m =n ?s ?p ?d ?f ?g ?h ?i ?k ?l ?m ?n >s >p >d >f >g >h >i >k >l >m >n"
else
  actc=''
  orb="1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 5g 6s 6p 6d 6f 6g 6h 7s 7p 7d 7f 7g 7h 7i 8s 8p 8d 8f 8g 8h 8i 8k 9s 9p 9d 9f 9g 9h 9i 9k 9l :s :p :d :f :g :h :i :k :l :m ;s ;p ;d ;f ;g ;h ;i ;k ;l ;m ;n <s <p <d <f <g <h <i <k <l <m <n =s =p =d =f =g =h =i =k =l =m =n ?s ?p ?d ?f ?g ?h ?i ?k ?l ?m ?n >s >p >d >f >g >h >i >k >l >m >n"
fi

order=""
if [ -e clist.ref ]
then
	echo "WARNING: clist.ref exists. Assuming customized subshell ordering"
	order="u"
fi

for i in $( seq 1 $2 )
do

  act=''
  line=$( head -$i $1 | tail -1 )
  echo $line
  for o in $orb
  do
    str=$(echo  $line | grep -o "${o}(.." )
    if [ ! "$str" == '' ]
    then
      occ=${str:4:5}
    else
      occ=0
    fi
  act=${act}${occ}${nl}
  done

  a='a'
  if [ $i == 1 ]
  then
    a=''
  fi
  act="${act} $3 $4 ${nl} 0${nl}"

jjgen > .bid 2>/dev/null <<!
${a}
${u}
15
n


15

${actc}${act}
!
grep "configuration state" .bid
rm .bid

mv clist.out clist.inp

done
mv clist.inp MR$2_RCI.c