Hi to everyone I have an awk script that calculate minimum distances between
points
## atom type frag - atom type surface
#!/bin/bash
FILE1=$1.lammpstrj
if [ -f $FILE1 ];
then
awk 'function sq(x) {
return x * x;
}
function dist(x1, y1, z1, x2, y2, z2) {
return sqrt(sq(x1 - x2) + sq(y1 - y2) + sq(z1 - z2));
}
function print_distances() {
if (na == 0)
print "No type 8 atoms.";
else {
min = 1000;
for (a = 0; a < na; a++) {
d = dist(x, y, z, pos[a,"x"], pos[a,"y"], pos[a,"z"]);
# printf "%7.5f ", d;
if (d < min) min = d;
}
printf "%6i %7.5f\n", istep, min;
x = y = z = 0;
delete pos;
na = 0;
}
}
$1 == 113 {
if (x || y || z)
print "More than one type $8 atom.";
else {
x = $2; y = $3; z = $4;
istep++;
}
}
$8 == 10 {
pos[na,"x"] = $2; pos[na,"y"] = $3; pos[na,"z"] = $4;
na += 1;
}
/^ITEM: ATOMS/ && na != 0 { print_distances(); }
END { print_distances(); }
' $1.lammpstrj > $1_mindist.txt
fi
where $1 is a particular atom and $8 is a other type of atoms
How could I prepare a python script
regards
A
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