def canonicalize(mf, mo_coeff, mo_occ, fock=None):
'''Canonicalization diagonalizes the UHF Fock matrix in occupied, virtual
subspaces separatedly (without change occupancy).
'''
mol = mf.mol
if not mol.symmetry:
return uhf.canonicalize(mf, mo_coeff, mo_occ, fock)
mo_occ = numpy.asarray(mo_occ)
assert(mo_occ.ndim == 2)
if fock is None:
dm = mf.make_rdm1(mo_coeff, mo_occ)
fock = mf.get_hcore() + mf.get_jk(mol, dm)
occidxa = mo_occ[0] == 1
occidxb = mo_occ[1] == 1
viridxa = mo_occ[0] == 0
viridxb = mo_occ[1] == 0
s = mf.get_ovlp()
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:,idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
c = numpy.dot(mo_coeff[:,idx], c)
cs[:,idx] = hf_symm._symmetrize_canonicalization_(mf.mol, e, c, s)
mo = numpy.empty_like(mo_coeff)
mo_e = numpy.empty(mo_occ.shape)
eig_(fock[0], mo_coeff[0], occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], viridxa, mo_e[0], mo[0])
eig_(fock[1], mo_coeff[1], occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], viridxb, mo_e[1], mo[1])
return mo_e, mo
def canonicalize(mf, mo_coeff, mo_occ, fock=None):
'''Canonicalization diagonalizes the UHF Fock matrix in occupied, virtual
subspaces separatedly (without change occupancy).
'''
if not mf.mol.symmetry:
return uhf.canonicalize(mf, mo_coeff, mo_occ, fock)
mo_occ = numpy.asarray(mo_occ)
assert(mo_occ.ndim == 2)
if fock is None:
dm = mf.make_rdm1(mo_coeff, mo_occ)
fock = mf.get_hcore() + mf.get_jk(mol, dm)
occidxa = mo_occ[0] == 1
occidxb = mo_occ[1] == 1
viridxa = mo_occ[0] == 0
viridxb = mo_occ[1] == 0
s = mf.get_ovlp()
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:,idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
c = numpy.dot(mo_coeff[:,idx], c)
cs[:,idx] = hf_symm._symmetrize_canonicalization_(mf.mol, e, c, s)
mo = numpy.empty_like(mo_coeff)
mo_e = numpy.empty(mo_occ.shape)
eig_(fock[0], mo_coeff[0], occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], viridxa, mo_e[0], mo[0])
eig_(fock[1], mo_coeff[1], occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], viridxb, mo_e[1], mo[1])
return mo_e, mo
def canonicalize(mf, mo_coeff, mo_occ, fock=None):
'''Canonicalization diagonalizes the UHF Fock matrix in occupied, virtual
subspaces separatedly (without change occupancy).
'''
mol = mf.mol
if not mol.symmetry:
return uhf.canonicalize(mf, mo_coeff, mo_occ, fock)
mo_occ = numpy.asarray(mo_occ)
assert (mo_occ.ndim == 2)
if fock is None:
dm = mf.make_rdm1(mo_coeff, mo_occ)
fock = mf.get_hcore() + mf.get_jk(mol, dm)
occidxa = mo_occ[0] == 1
occidxb = mo_occ[1] == 1
viridxa = ~occidxa
viridxb = ~occidxb
mo = numpy.empty_like(mo_coeff)
mo_e = numpy.empty(mo_occ.shape)
if (hasattr(mo_coeff, 'orbsym') or
(hasattr(mo_coeff[0], 'orbsym') and hasattr(mo_coeff[1], 'orbsym'))):
orbsyma, orbsymb = get_orbsym(mol, mo_coeff)
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:, idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
cs[:, idx] = numpy.dot(mo_coeff[:, idx], c)
for ir in set(orbsyma):
idx_ir = orbsyma == ir
eig_(fock[0], mo_coeff[0], idx_ir & occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], idx_ir & viridxa, mo_e[0], mo[0])
for ir in set(orbsymb):
idx_ir = orbsymb == ir
eig_(fock[1], mo_coeff[1], idx_ir & occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], idx_ir & viridxb, mo_e[1], mo[1])
else:
s = mf.get_ovlp()
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:, idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
c = numpy.dot(mo_coeff[:, idx], c)
cs[:, idx] = hf_symm._symmetrize_canonicalization_(mf, e, c, s)
eig_(fock[0], mo_coeff[0], occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], viridxa, mo_e[0], mo[0])
eig_(fock[1], mo_coeff[1], occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], viridxb, mo_e[1], mo[1])
orbsyma, orbsymb = uhf_symm.get_orbsym(mol, mo, s, False)
mo = hf_symm.attach_orbsym(mo, (orbsyma, orbsymb))
return mo_e, mo
def canonicalize(mf, mo_coeff, mo_occ, fock=None):
'''Canonicalization diagonalizes the UHF Fock matrix in occupied, virtual
subspaces separatedly (without change occupancy).
'''
mol = mf.mol
if not mol.symmetry:
return uhf.canonicalize(mf, mo_coeff, mo_occ, fock)
mo_occ = numpy.asarray(mo_occ)
assert(mo_occ.ndim == 2)
if fock is None:
dm = mf.make_rdm1(mo_coeff, mo_occ)
fock = mf.get_hcore() + mf.get_veff(mf.mol, dm)
occidxa = mo_occ[0] == 1
occidxb = mo_occ[1] == 1
viridxa = ~occidxa
viridxb = ~occidxb
mo = numpy.empty_like(mo_coeff)
mo_e = numpy.empty(mo_occ.shape)
if (getattr(mo_coeff, 'orbsym', None) is not None or
(getattr(mo_coeff[0], 'orbsym', None) is not None and
getattr(mo_coeff[1], 'orbsym', None) is not None)):
orbsyma, orbsymb = get_orbsym(mol, mo_coeff)
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:,idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
cs[:,idx] = numpy.dot(mo_coeff[:,idx], c)
for ir in set(orbsyma):
idx_ir = orbsyma == ir
eig_(fock[0], mo_coeff[0], idx_ir & occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], idx_ir & viridxa, mo_e[0], mo[0])
for ir in set(orbsymb):
idx_ir = orbsymb == ir
eig_(fock[1], mo_coeff[1], idx_ir & occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], idx_ir & viridxb, mo_e[1], mo[1])
else:
s = mf.get_ovlp()
def eig_(fock, mo_coeff, idx, es, cs):
if numpy.count_nonzero(idx) > 0:
orb = mo_coeff[:,idx]
f1 = reduce(numpy.dot, (orb.T.conj(), fock, orb))
e, c = scipy.linalg.eigh(f1)
es[idx] = e
c = numpy.dot(mo_coeff[:,idx], c)
cs[:,idx] = hf_symm._symmetrize_canonicalization_(mf, e, c, s)
eig_(fock[0], mo_coeff[0], occidxa, mo_e[0], mo[0])
eig_(fock[0], mo_coeff[0], viridxa, mo_e[0], mo[0])
eig_(fock[1], mo_coeff[1], occidxb, mo_e[1], mo[1])
eig_(fock[1], mo_coeff[1], viridxb, mo_e[1], mo[1])
orbsyma, orbsymb = get_orbsym(mol, mo, s, False)
mo = (lib.tag_array(mo[0], orbsym=orbsyma),
lib.tag_array(mo[1], orbsym=orbsymb))
return mo_e, mo