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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
C1=lo.orth.orth_ao(mol1,method='lowdin')


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

#Lowdin orthogonalization of the ao basis
C2=lo.orth.orth_ao(mol2,method='lowdin')

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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  • $\begingroup$ First of all, do you need the eri's in MO or AO basis. Firstly, you can try with supermolecular approach and both fragment approach and see what you are getting. After that, you can convert them to MO basis. Although it is not exactly your answer, but try to compare them. It will be better with a smaller basis set ofcourse. $\endgroup$
    – Pro
    Commented Feb 8 at 12:15

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