Here are 3 python test files for computing both the atomic and molecular orbitals (MOs) overlap matrices.
In computing the MOs overlap, we need to make sure that the diagonal elements of the MO overlap matrix are all 1.
All the details are explicitly explained in the files.
test.py
This file tests the Libint2 library in Libra for computing the atomic orbital overlap matrix.
test_molden.py
This file computes the MO overlaps from a molden file format printed out by CP2K.
test_molog.py
This file computes the MO overlaps from a MOLog file printed out by CP2K.