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contcar2xyz.sh
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contcar2xyz.sh
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#!/bin/bash
#
# Convert a VASP POSCAR file into the xyz format.
#
# Usage
if [ ! -n "$2" ]; then
echo "Usage: `basename $0` [CONTCAR file] [xyz file]"
exit
fi
# the input and output file names given as command-line parameters
contcar=$1
xyz=$2
rm -f $xyz
# get the scaling factor and the lattice vectors
scalfact=$(awk '{n=n+1; if (n==2){print $1; exit} }' $contcar)
xsize=$(awk '{n=n+1; if(n==3){print $1; exit} }' $contcar)
ysize=$(awk '{n=n+1; if(n==4){print $2; exit} }' $contcar)
zsize=$(awk '{n=n+1; if(n==5){print $3; exit} }' $contcar)
# multiply the lattice vectors by the scaling factor
xsize=$( echo "$xsize*$scalfact" | bc -l)
ysize=$( echo "$ysize*$scalfact" | bc -l)
zsize=$( echo "$zsize*$scalfact" | bc -l)
# get the number of atoms
natoms=$(awk 'BEGIN{sum=0}{n=n+1; if(n==7){ for(i=1; i<=NF; i++){sum=sum+$i}}}END{print sum}' $contcar)
# are we direct or cartesian
if [[ -n "$(grep -i selective $contcar)" ]];
then
format=$(awk '{n=n+1; if(n==9){print $1} }' $contcar)
selectiveDynamics=1
else
format=$(awk '{n=n+1; if(n==8){print $1} }' $contcar)
selectiveDynamics=0
fi
if [ "$format" == "Direct" ]; then
isdirect=1
else
isdirect=0
fi
# create the xyz file
# number of atoms
echo $natoms > $xyz
# header with cell size
printf "Frame number 1 1 fs boxsize %8.3f %8.3f %8.3f\n" $xsize $ysize $zsize >> $xyz
#
# selective dynamics or not
#
if [[ selectiveDynamics -eq 0 ]];
then
#
# coordinates, from either direct or cartesian format
#
if [ $isdirect -eq 1 ]; then
awk -v selectiveDynamics=$selectiveDynamics -v xsize=$xsize -v ysize=$ysize -v zsize=$zsize 'BEGIN{j=1; k=1; n=0; natoms=0}{
n=n+1;
if(n==6){for(i=1; i<=NF; i++){types[i]=$i}};
if(n==7){for(i=1; i<=NF; i++){ntypes[i]=$i; natoms=natoms+$i}; numberoftypes=i};
# create a simple natoms long array typelist with the types in the right order
# loop over types
for(i=1; i<=numberoftypes; i++) {
# loop over number of atoms of this type
for(l=1; l<=ntypes[i]; l++) {
typelist[j] = types[i];
j++;
}
}
if(n>8 && n<=8+natoms){ print typelist[k], $1*xsize, $2*ysize, $3*zsize, "1"; k++};
}' $contcar >> $xyz
else
awk -v scalfact=$scalfact -v xsize=$xsize -v ysize=$ysize -v zsize=$zsize 'BEGIN{j=1; k=1; n=0; natoms=0}{
n=n+1;
if(n==6){for(i=1; i<=NF; i++){types[i]=$i}};
if(n==7){for(i=1; i<=NF; i++){ntypes[i]=$i; natoms=natoms+$i}; numberoftypes=i};
# create a simple natoms long array typelist with the types in the right order
# loop over types
for(i=1; i<=numberoftypes; i++) {
# loop over number of atoms of this type
for(l=1; l<=ntypes[i]; l++) {
typelist[j] = types[i];
j++;
}
}
if(n>8 && n<=8+natoms){ print typelist[k], $1*scalfact, $2*scalfact, $3*scalfact, "1"; k++};
}' $contcar >> $xyz
fi
else
#
# coordinates, from either direct or cartesian format
#
if [ $isdirect -eq 1 ]; then
awk -v selectiveDynamics=$selectiveDynamics -v xsize=$xsize -v ysize=$ysize -v zsize=$zsize 'BEGIN{j=1; k=1; n=0; natoms=0}{
n=n+1;
if(n==6){for(i=1; i<=NF; i++){types[i]=$i}};
if(n==7){for(i=1; i<=NF; i++){ntypes[i]=$i; natoms=natoms+$i}; numberoftypes=i};
# create a simple natoms long array typelist with the types in the right order
# loop over types
for(i=1; i<=numberoftypes; i++) {
# loop over number of atoms of this type
for(l=1; l<=ntypes[i]; l++) {
typelist[j] = types[i];
j++;
}
}
if(n>9 && n<=9+natoms){ print typelist[k], $1*xsize, $2*ysize, $3*zsize, "1"; k++};
}' $contcar >> $xyz
else
awk -v scalfact=$scalfact -v xsize=$xsize -v ysize=$ysize -v zsize=$zsize 'BEGIN{j=1; k=1; n=0; natoms=0}{
n=n+1;
if(n==6){for(i=1; i<=NF; i++){types[i]=$i}};
if(n==7){for(i=1; i<=NF; i++){ntypes[i]=$i; natoms=natoms+$i}; numberoftypes=i};
# create a simple natoms long array typelist with the types in the right order
# loop over types
for(i=1; i<=numberoftypes; i++) {
# loop over number of atoms of this type
for(l=1; l<=ntypes[i]; l++) {
typelist[j] = types[i];
j++;
}
}
if(n>9 && n<=9+natoms){ print typelist[k], $1*scalfact, $2*scalfact, $3*scalfact, "1"; k++};
}' $contcar >> $xyz
fi
fi
exit 0;