wrap_xyz_file.xyz

#!/bin/bash
#
# Take an xyz (movie) file and wrap the coordinates back to the
# periodic supercell. NB! Assumes an orthogonal supercell and that the
# cell size is given by the three last fields of the second row of the
# xyz file.
#
# Eero Holmstrom, 2016
#

# usage
if [[ -z "$4" ]];
then
    echo "Usage: $(basename $0) [file.xyz] [x0] [y0] [z0]"
    exit 1;
fi

# assign input parameters
infile=$1
x0=$2
y0=$3
z0=$4

if [[ ! -e $infile ]];
then
    echo "File $infile not found! Exiting."
    exit 1;
fi

# find size of supercell
xsize=$(awk '{n++}(n==2){print $(NF-2)}' $infile)
ysize=$(awk '{n++}(n==2){print $(NF-1)}' $infile)
zsize=$(awk '{n++}(n==2){print $(NF)}' $infile)

echo ""
printf "Found periodic supercell of dimensions %5.8f A, %5.8f A, %5.8f A.\n" $xsize $ysize $zsize
printf "Using %5.8f A, %5.8f A, %5.8f A as the origin.\n" $x0 $y0 $z0
echo ""

echo "Now wrapping given xyz movie to the given supercell..."

awk -v x0=$x0 -v y0=$y0 -v z0=$z0 -v xsize=$xsize -v ysize=$ysize -v zsize=$zsize 'BEGIN{natoms=-999; n=0;}

{n++;}
(n==natoms+3){n=1;}

(n==1){natoms=$1; print natoms}
(n==2){print $0, "wrapped to supercell of size", xsize, ysize, zsize}
(n>=3){type=$1; x=$2; y=$3; z=$4;

if(x<x0) {for(i=1; x<x0; i++){x=x+xsize}} else if(x>=x0+xsize) {for(i=1; x>=x0+xsize; i++){x=x-xsize}};
if(y<y0) {for(i=1; y<y0; i++){y=y+ysize}} else if(y>=y0+ysize) {for(i=1; y>=y0+ysize; i++){y=y-ysize}};
if(z<z0) {for(i=1; z<z0; i++){z=z+zsize}} else if(z>=z0+zsize) {for(i=1; z>=z0+zsize; i++){z=z-zsize}};

print type, x, y, z;

}' $infile > $infile.wrapped.xyz

echo "Done. Wrapped trajectory output to $infile.wrapped.xyz"
echo ""
echo "Exiting."
echo ""

exit 0;