Shell Programming and Scripting

# $NoFrames and $NoAtoms are defined earlier in the code and do not change
#
# Start of the systematic loop, outer deals with frames, inner with atoms
#
FrameNumber=0 # Used to know which line the sed statement should strip out
FrameCounter=1 # Keeps a track of which frame we're analysing
AtomCounter=1 # Keeps a track of which atom (within each frame) we're analysing
while [[ $FrameCounter -le $NoFrames ]]; do
        while [[ $AtomCounter -le $NoAtoms ]]; do
                let "AdjustedAtomCounter=(($FrameNumber*($NoAtoms+2))+($AtomCounter+2))" # This line should allow me to skip the first two lines per frame (the comment lines)
                sed -n "${AdjustedAtomCounter}p" *.xyz
                let "AtomCounter=$AtomCounter+1"
        done
echo $NoAtoms >> Cartesian.xyz
echo "Cartesian GeomOpt Video" >> Cartesian.xyz
let FrameCounter=FrameCounter+1
let FrameNumber=FrameNumber+1
let AtomCounter=1
done
rm *.txt
exit

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Cartesian GeomOpt Video
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Cartesian GeomOpt Video
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#!/usr/bin/env ksh

# converts coordinates from one form to another and
# echos translated values
function transform
{ 
    echo "$(( $1 * 300 ))  $(( $2 * 200 )) $(( $3 /42 ))"
}

natoms=5       # constant number of atoms/frame
nframes=2       # number of frames in the input data
data=t37.data   # name of the data file (my test file was t37.data)

for (( j = 0; j < nframes; j++ ))         # for each frame
do
    read junk       # read and ignore comment lines 
    read junk

    echo "Cartesian GeomOpt Video"  # looks like this marks the frame in new file????
    for (( i = 0; i < natoms; i++ ))     # for each atom in the frame
    do
        read atom_letter x y z           # read its data 
        echo "$atom_letter $(transform $x $y $z)"   # transform and wriite 
    done
done <$data >Cartesian.xyz   # all echos in the loop write to cart.xyz

sed -n "${AdjustedAtomCounter}p" *.xyz