count.

#!/bin/bash -l
#=====================================================
# count.     ### count pore water molecules and    ###
#            ### ions                              ###
# parameters
# $1         processing option
#   options: <null> - count everything
#            T  - count everything in channel 0 (top)
#            t  - count waters in channel 0
#            ti - count ions in channel 0
#            B  - count everything in channel 1 (bot)
#            t  - count waters in channel 1
#            ti - count ions in channel 1
#_____________________________________________________

declare -a fyles
fyles=(twat twatt tca tan tcat tant bwat bwatt bca ban bcat bant)

i=0
last=11
if [ "${1}" == "T" ]; then
  last=5
elif [ "${1}" == "t" ]; then
  last=1
elif [ "${1}" == "ti" ]; then
  i=2
  last=5
elif [ "${1}" == "B" ]; then
  i=6
elif [ "${1}" == "b" ]; then
  i=6
  last=7
elif [ "${1}" == "bi" ]; then
  i=8
fi

while [ ${i} -le ${last} ]; do
  if [ -a ${fyles[$i]}.xvg ]; then rm ${fyles[$i]}.xvg; fi
  source ../jobs/select. ${fyles[$i]}
  let "i=i+1"
done

for i in {0..1} {6..7}; do
  source ../jobs/stddev.awk ${fyles[$i]}.xvg > ${fyles[$i]}.std
done