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Fix variable assignment mypy error localization #287

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Fix variable assignment mypy error localization #287

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28d873e
remove two ignore[assignment] flags
cariluo Aug 27, 2026
1d5ccf1
rename S_ and W to unr_S_ and W_unr
cariluo Aug 27, 2026
9133e23
Merge branch 'main' into fix_variable_assignment_mypy_error_localization
cariluo Aug 27, 2026
87e9445
use a and b naming and add helper function
cariluo Aug 27, 2026
106856a
pass W so that I can use helper in boys branch
cariluo Aug 27, 2026
0361b56
Merge branch 'main' into fix_variable_assignment_mypy_error_localization
cariluo Sep 2, 2026
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75 changes: 30 additions & 45 deletions src/quemb/molbe/mbe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1353,6 +1353,28 @@ def read_heff(self, heff_file="bepotfile.h5"):
for fobj in self.Fobjs:
fobj.heff = filepot.get(fobj.dname)

def _get_noncore_W(self, W, P_core, pop_thr=0.7):
"""Construct an orthonormal working basis with core orbitals removed."""

# Project out columns of W with core character
P_noncore = eye(W.shape[0]) - P_core @ self.S
C = P_noncore @ W

# Decide which columns of W to retain
# NOTE: PYSCF has basis in 1s2s3s2p2p2p3p3p3p format
# fix no_core_idx - use population for now
Cpop = multi_dot((C.T, self.S, C))
no_core_idx = where(diag(Cpop) > pop_thr)[0]
C = C[:, no_core_idx]

# Perform symmetric (Lowdin) othogonalization
S_ = multi_dot((C.T, self.S, C))
es_, vs_ = eigh(S_)
s_ = diag(1.0 / sqrt(es_))
W_ = multi_dot((vs_, s_, vs_.T))

return C @ W_

def localize(
self,
lo_method: LocMethods,
Expand Down Expand Up @@ -1399,48 +1421,22 @@ def localize(
self.W = vs_[:, edx] / sqrt(es_[edx]) @ vs_[:, edx].T
if self.frozen_core:
if self.unrestricted:
P_core = [
eye(self.W.shape[0]) - (self.P_core[s] @ self.S) for s in [0, 1]
]
C_ = P_core @ self.W
unr_Cpop = [multi_dot((C_[s].T, self.S, C_[s])) for s in [0, 1]]
unr_Cpop = [diag(unr_Cpop[s]) for s in [0, 1]]
unr_no_core_idx = [where(unr_Cpop[s] > 0.7)[0] for s in [0, 1]]
C_ = [C_[s][:, unr_no_core_idx[s]] for s in [0, 1]]
S_ = [multi_dot((C_[s].T, self.S, C_[s])) for s in [0, 1]]
unr_W_ = []
for s in [0, 1]:
es_, vs_ = eigh(S_[s])
s_ = sqrt(es_)
s_ = diag(1.0 / s_)
unr_W_.append(multi_dot((vs_, s_, vs_.T)))
self.W = [C_[s] @ unr_W_[s] for s in [0, 1]]
self.W_a = self._get_noncore_W(self.W, self.P_core[0], pop_thr=0.7)
self.W_b = self._get_noncore_W(self.W, self.P_core[1], pop_thr=0.7)
else:
P_core = eye(self.W.shape[0]) - self.P_core @ self.S
C_ = P_core @ self.W
# NOTE: PYSCF has basis in 1s2s3s2p2p2p3p3p3p format
# fix no_core_idx - use population for now
Cpop = multi_dot((C_.T, self.S, C_))
no_core_idx = where(diag(Cpop) > 0.7)[0]
C_ = C_[:, no_core_idx]
S_ = multi_dot((C_.T, self.S, C_)) # type: ignore[assignment]
es_, vs_ = eigh(S_)
s_ = sqrt(es_)
s_ = diag(1.0 / s_)
W_ = multi_dot((vs_, s_, vs_.T))
self.W = C_ @ W_
self.W = self._get_noncore_W(self.W, self.P_core, pop_thr=0.7)

if self.unrestricted:
if self.frozen_core:
self.lmo_coeff_a = multi_dot(
(self.W[0].T, self.S, self.C_a[:, self.ncore :]) # type: ignore[attr-defined]
(self.W_a.T, self.S, self.C_a[:, self.ncore :]) # type: ignore[attr-defined]
)
self.lmo_coeff_b = multi_dot(
(self.W[1].T, self.S, self.C_b[:, self.ncore :]) # type: ignore[attr-defined]
(self.W_b.T, self.S, self.C_b[:, self.ncore :]) # type: ignore[attr-defined]
)
else:
self.lmo_coeff_a = multi_dot((self.W.T, self.S, self.C_a)) # type: ignore[attr-defined]
self.lmo_coeff_b = multi_dot((self.W.T, self.S, self.C_b)) # type: ignore[attr-defined]
self.lmo_coeff_a = multi_dot((self.W_unr.T, self.S, self.C_a)) # type: ignore[attr-defined]
self.lmo_coeff_b = multi_dot((self.W_unr.T, self.S, self.C_b)) # type: ignore[attr-defined]
else:
if self.frozen_core:
self.lmo_coeff = multi_dot(
Expand All @@ -1454,18 +1450,7 @@ def localize(
edx = es_ > 1.0e-15
W_ = vs_[:, edx] / sqrt(es_[edx]) @ vs_[:, edx].T
if self.frozen_core:
P_core = eye(W_.shape[0]) - self.P_core @ self.S
C_ = P_core @ W_
Cpop = multi_dot((C_.T, self.S, C_))
Cpop = diag(Cpop)
no_core_idx = where(Cpop > 0.55)[0]
C_ = C_[:, no_core_idx]
S_ = multi_dot((C_.T, self.S, C_)) # type: ignore[assignment]
es_, vs_ = eigh(S_)
s_ = sqrt(es_)
s_ = diag(1.0 / s_)
W_ = multi_dot((vs_, s_, vs_.T))
W_ = C_ @ W_
W_ = self._get_noncore_W(W_, self.P_core, pop_thr=0.55)

self.W = get_loc(
self.mf.mol,
Expand Down
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