I am trying to compute integrals of the form $(pq|rs)$ where the orbitals $p$ and $q$ are orthogonalized atomic orbitals for a fragment $A$ and $r,s$ are orthogonalized on fragment $B$. I was thinking of a setup similar to this

from pyscf import gto, scf, dft, ao2mo, lo
import numpy as np

#BASIS SET: (4s) -> [2s]
mol1 = gto.M(atom='He 0 0 0', basis='6-31g')

#Lowdin orthogonalization of the ao basis

mol2 = gto.M(atom='He 2 0 0', basis='6-31g')

#Lowdin orthogonalization of the ao basis

This snippet will create two separate molecule instances with their corresponding $C$ orthogonalization matrix (the same in this situation).

Is there a way to either take these two molecule instances and calculate the two-electron integrals between them? Or do I create a "supramolecular" system instead, compute all two-electron integrals, and somehow sort them with respect to the centers of the AOs? If the latter, how to do this?



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