Dear all.

I am currently trying to find the shortest interatomic distance in a cell.
This is because we are trying to predict the electrical properties of metals and crystals from that value (although there are others).

I think sample file of Materials Script(ex. CalcUniqueBondLengthAngles.pl), but this code wasn't helpful as it's supposed to contain join information(use "collection = source->Bonds").

How to calculate the minimum distance between atom(Atoms Distance under fig.)??

Thank You!

PS(2020/12/01).
I write this code.
This code's flow is
"select two atoms -> calculate distance -> remove Duplicate value"

However, this code is heavy because it calculates (ex. A_B and B_A) for all combinations.
Can you give me some advice on how to improve this code and make it lighter?

#!perl
use strict;
use warnings;
use MaterialsScript qw(:all);

use Math::Trig;

sub Length {
  my (\\\$atom1, \\\$atom2) = @_;
  return sqrt((\\\$atom1->X - \\\$atom2->X)**2 + (\\\$atom1->Y - \\\$atom2->Y)**2 + (\\\$atom1->Z - \\\$atom2->Z)**2);
}

my \\\$doc = \\\$Documents{"urea.xsd"};
my \\\$atoms = \\\$doc->AsymmetricUnit->Atoms;
my (\\\$name1, \\\$name2, \\\$length, @lengths);

for (my \\\$i=0; \\\$i<\\\$atoms->Count; ++\\\$i) {
    my \\\$atom1 = \\\$doc->AsymmetricUnit->Atoms(\\\$i);
    for (my \\\$j=0; \\\$j<\\\$atoms->Count; ++\\\$j) {
    my \\\$atom2 = \\\$doc->AsymmetricUnit->Atoms(\\\$j);
    if (\\\$atom1->X == \\\$atom2->X and \\\$atom1->Y == \\\$atom2->Y and \\\$atom1->Z == \\\$atom2->Z){
        next;
    }
    \\\$length = Length(\\\$atom1, \\\$atom2);
    push(@lengths, \\\$length);
    }
}

my %uniq = map {\\\$_ => 1} @lengths;
my @uniq_lengths = keys %uniq;

@uniq_lengths = sort{\\\$a <=> \\\$b} @uniq_lengths;
print "first   min ".\\\$uniq_lengths[0]."\\n";
print "secound min ".\\\$uniq_lengths[1]."\\n";
print "therd   min ".\\\$uniq_lengths[2]."\\n";