source: util/src/CalculateMass.sh@ 0ab37b

#!/bin/sh
#
# calculates mass of a molecule in a XYZ file

ELEMENTSDB="/home/heber/workspace/ESPACK/bin/elements.db"

if [ -z "$1" ]; then
        echo "Usage $0 <XYZ file>"
        exit 1
else
        XYZ="$1"
        if [ ! -e $XYZ ]; then
                echo "The xyz file $XYZ does not exist!"
                exit 1
        fi      
fi

# check for db presence
if [ ! -e $ELEMENTSDB ]; then
        echo "The database file $ELEMENTSDB does not exist!"
        exit 1
fi      

elements=(`grep -v ^# ${ELEMENTSDB} | awk -F" " {'print $2'}`)
masses=(`grep -v ^# ${ELEMENTSDB} | awk -F" " {'print $7'}`)

i=0
totalmass=0
while [ $i -lt ${#elements[*]} ]; do
        nr=`grep -E "^${elements[$i]}[[:space:]]+" $XYZ | wc -l`
        totalmass=`echo "$totalmass $nr ${masses[$i]}" | awk -F" " {'print $1+$2*$3'}`
        let i=$i+1
done

echo "Totalmass is $totalmass atomicunits"
exit 0