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The issue has to do with how the exchange divergence correction (using the probe-charge Ewald Madelung constant correction) is handled in periodic HF, and whether one views this as a modification of the integrals or as an additive correction to the total energy. Separately, note that you don't need to think about a "cell" and a "supercell" separately here, since you're always doing a Gamma point calculation. Here's a cleaned up version,

import numpy
from pyscf.pbc import scf as pbcscf
from pyscf.pbc import gto as pbcgto
from pyscf import fci
from pyscf.pbc import tools

N = 8  # atoms in the cell
r = 2.0

cell = pbcgto.M(
      unit = 'B',
      a = [[N*r, 0.0, 0.0], [0, 1, 0], [0, 0, 1]]…

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@AndrewLiu0725
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@tberkel
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Answer selected by AndrewLiu0725
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