A little script that prints out possible permutations of the like atoms in simple molecule(s). The molecule(s) here is something like [H2O]3 or [H2O]2[Na]2. For [H2O]2 (water dimer), for example, the output is as follows:

#
# input = '[H2O]2'
#
#  2 of 'H2O' (3 atoms : H H O)
#
# molecules:
#
#  0 -> H2O
#  1 -> H2O
#
# permutations of the molecules:
#
#  0 1
#  1 0
#
# atoms:
#
#  0 -> H
#  1 -> H
#  2 -> O
#  3 -> H
#  4 -> H
#  5 -> O
#
# permutations of the atoms for a fixed order of the molecules:
#
#  0 1 2 3 4 5
#  0 1 2 4 3 5
#  1 0 2 3 4 5
#  1 0 2 4 3 5
#
# permutations of the atoms for different arrangements of the molecules:
#
0 1 2 3 4 5
0 1 2 4 3 5
1 0 2 3 4 5
1 0 2 4 3 5
3 4 5 0 1 2
4 3 5 0 1 2
3 4 5 1 0 2
4 3 5 1 0 2
# 8 total

Download the script here or run it via CGI: