from __future__ import division, print_function
import numpy as np
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[docs]def overlap_ni(me, sp1,R1, sp2,R2, **kw):
"""
Computes overlap for an atom pair. The atom pair is given by a pair of species indices
and the coordinates of the atoms.
Args:
sp1,sp2 : specie indices, and
R1,R2 : respective coordinates in Bohr, atomic units
Result:
matrix of orbital overlaps
The procedure uses the numerical integration in coordinate space.
"""
from pynao.m_ao_matelem import build_3dgrid
from pynao.m_ao_eval_libnao import ao_eval_libnao as ao_eval #_libnao
grids = build_3dgrid(me, sp1, R1, sp2, R2, **kw)
ao1 = ao_eval(me.ao1, R1, sp1, grids.coords)
ao1 = ao1 * grids.weights
ao2 = ao_eval(me.ao2, R2, sp2, grids.coords)
overlaps = np.einsum("ij,kj->ik", ao1, ao2) # overlaps = np.matmul(ao1, ao2.T)
return overlaps