def project_mo_nr2nr(mol1, mo1, mol2):
r''' Project orbital coefficients from basis set 1 (C1 for mol1) to basis
set 2 (C2 for mol2).
.. math::
|\psi1\rangle = |AO1\rangle C1
|\psi2\rangle = P |\psi1\rangle = |AO2\rangle S^{-1}\langle AO2| AO1\rangle> C1 = |AO2\rangle> C2
C2 = S^{-1}\langle AO2|AO1\rangle C1
There are three relevant functions:
:func:`project_mo_nr2nr` is the projection for non-relativistic (scalar) basis.
:func:`project_mo_nr2r` projects from non-relativistic to relativistic basis.
:func:`project_mo_r2r` is the projection between relativistic (spinor) basis.
'''
s22 = mol2.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', mol2, mol1)
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
return lib.cho_solve(s22, numpy.dot(s21, mo1), strict_sym_pos=False)
else:
return [
lib.cho_solve(s22, numpy.dot(s21, x), strict_sym_pos=False)
for x in mo1
]
def project_mo_r2r(mol1, mo1, mol2):
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
t22 = mol2.intor_symmetric('int1e_spsp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', mol2, mol1)
t21 = mole.intor_cross('int1e_spsp_spinor', mol2, mol1)
n2c = s21.shape[1]
pl = lib.cho_solve(s22, s21)
ps = lib.cho_solve(t22, t21)
return numpy.vstack((numpy.dot(pl, mo1[:n2c]), numpy.dot(ps, mo1[n2c:])))
def project_mo_r2r(mol1, mo1, mol2):
s22 = mol2.intor_symmetric('cint1e_ovlp')
t22 = mol2.intor_symmetric('cint1e_spsp')
s21 = mole.intor_cross('cint1e_ovlp', mol2, mol1)
t21 = mole.intor_cross('cint1e_spsp', mol2, mol1)
n2c = s21.shape[1]
pl = lib.cho_solve(s22, s21)
ps = lib.cho_solve(t22, t21)
return numpy.vstack((numpy.dot(pl, mo1[:n2c]),
numpy.dot(ps, mo1[n2c:])))
def project_dm_r2r(mol1, dm1, mol2):
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
t22 = mol2.intor_symmetric('int1e_spsp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', mol2, mol1)
t21 = mole.intor_cross('int1e_spsp_spinor', mol2, mol1)
pl = lib.cho_solve(s22, s21, strict_sym_pos=False)
ps = lib.cho_solve(t22, t21, strict_sym_pos=False)
p21 = scipy.linalg.block_diag(pl, ps)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def project_mo_r2r(mol1, mo1, mol2):
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
t22 = mol2.intor_symmetric('int1e_spsp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', mol2, mol1)
t21 = mole.intor_cross('int1e_spsp_spinor', mol2, mol1)
n2c = s21.shape[1]
pl = lib.cho_solve(s22, s21, strict_sym_pos=False)
ps = lib.cho_solve(t22, t21, strict_sym_pos=False)
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
return numpy.vstack((numpy.dot(pl, mo1[:n2c]),
numpy.dot(ps, mo1[n2c:])))
else:
return [numpy.vstack((numpy.dot(pl, x[:n2c]),
numpy.dot(ps, x[n2c:]))) for x in mo1]
def project_dm_r2r(mol1, dm1, mol2):
__doc__ = project_dm_nr2nr.__doc__
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
t22 = mol2.intor_symmetric('int1e_spsp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', mol2, mol1)
t21 = mole.intor_cross('int1e_spsp_spinor', mol2, mol1)
n2c = s21.shape[1]
pl = lib.cho_solve(s22, s21)
ps = lib.cho_solve(t22, t21)
p21 = scipy.linalg.block_diag(pl, ps)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def project_mo_nr2r(mol1, mo1, mol2):
assert(not mol1.cart)
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_sph', mol2, mol1)
ua, ub = mol2.sph2spinor_coeff()
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
mo2 = numpy.dot(s21, mo1)
return lib.cho_solve(s22, mo2, strict_sym_pos=False)
else:
return [lib.cho_solve(s22, numpy.dot(s21, x), strict_sym_pos=False)
for x in mo1]
def project_dm_nr2nr(mol1, dm1, mol2):
r''' Project density matrix representation from basis set 1 (mol1) to basis
set 2 (mol2).
.. math::
|AO2\rangle DM_AO2 \langle AO2|
= |AO2\rangle P DM_AO1 P \langle AO2|
DM_AO2 = P DM_AO1 P
P = S_{AO2}^{-1}\langle AO2|AO1\rangle
There are three relevant functions:
:func:`project_dm_nr2nr` is the projection for non-relativistic (scalar) basis.
:func:`project_dm_nr2r` projects from non-relativistic to relativistic basis.
:func:`project_dm_r2r` is the projection between relativistic (spinor) basis.
'''
s22 = mol2.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', mol2, mol1)
p21 = lib.cho_solve(s22, s21)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def project_mo_r2r(mol1, mo1, mol2):
__doc__ = project_mo_nr2nr.__doc__
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
t22 = mol2.intor_symmetric('int1e_spsp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', mol2, mol1)
t21 = mole.intor_cross('int1e_spsp_spinor', mol2, mol1)
n2c = s21.shape[1]
pl = lib.cho_solve(s22, s21)
ps = lib.cho_solve(t22, t21)
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
return numpy.vstack((numpy.dot(pl, mo1[:n2c]),
numpy.dot(ps, mo1[n2c:])))
else:
return [numpy.vstack((numpy.dot(pl, x[:n2c]),
numpy.dot(ps, x[n2c:]))) for x in mo1]
def project_mo_nr2r(mol1, mo1, mol2):
__doc__ = project_mo_nr2nr.__doc__
assert(not mol1.cart)
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_sph', mol2, mol1)
ua, ub = mol2.sph2spinor_coeff()
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
mo2 = numpy.dot(s21, mo1)
return lib.cho_solve(s22, mo2)
else:
return [lib.cho_solve(s22, numpy.dot(s21, x)) for x in mo1]
def project(mfmo, init_mo, ncore, s):
s_init_mo = numpy.einsum('pi,pi->i', init_mo.conj(), s.dot(init_mo))
if abs(s_init_mo -
1).max() < 1e-7 and mfmo.shape[1] == init_mo.shape[1]:
# Initial guess orbitals are orthonormal
return init_mo
# TODO: test whether the canonicalized orbitals are better than the projected orbitals
# Be careful that the ordering of the canonicalized orbitals may be very different
# to the CASSCF orbitals.
# else:
# fock = casscf.get_fock(mc, init_mo, casscf.ci)
# return casscf._scf.eig(fock, s)[1]
nocc = ncore + casscf.ncas
if ncore > 0:
mo0core = init_mo[:, :ncore]
s1 = reduce(numpy.dot, (mfmo.T, s, mo0core))
s1core = reduce(numpy.dot, (mo0core.T, s, mo0core))
coreocc = numpy.einsum('ij,ji->i', s1, lib.cho_solve(s1core, s1.T))
coreidx = numpy.sort(numpy.argsort(-coreocc)[:ncore])
logger.debug(casscf, 'Core indices %s', coreidx)
logger.debug(casscf, 'Core components %s', coreocc[coreidx])
# take HF core
mocore = mfmo[:, coreidx]
# take projected CAS space
mocas = init_mo[:,ncore:nocc] \
- reduce(numpy.dot, (mocore, mocore.T, s, init_mo[:,ncore:nocc]))
mocc = lo.orth.vec_lowdin(numpy.hstack((mocore, mocas)), s)
else:
mocc = lo.orth.vec_lowdin(init_mo[:, :nocc], s)
# remove core and active space from rest
if mocc.shape[1] < mfmo.shape[1]:
if casscf.mol.symmetry:
restorb = []
orbsym = scf.hf_symm.get_orbsym(casscf.mol, mfmo, s)
for ir in set(orbsym):
mo_ir = mfmo[:, orbsym == ir]
rest = mo_ir - reduce(numpy.dot, (mocc, mocc.T, s, mo_ir))
e, u = numpy.linalg.eigh(
reduce(numpy.dot, (rest.T, s, rest)))
restorb.append(numpy.dot(rest, u[:, e > 1e-7]))
restorb = numpy.hstack(restorb)
else:
rest = mfmo - reduce(numpy.dot, (mocc, mocc.T, s, mfmo))
e, u = numpy.linalg.eigh(reduce(numpy.dot, (rest.T, s, rest)))
restorb = numpy.dot(rest, u[:, e > 1e-7])
mo = numpy.hstack((mocc, restorb))
else:
mo = mocc
if casscf.verbose >= logger.DEBUG:
s1 = reduce(numpy.dot, (mo[:, ncore:nocc].T, s, mfmo))
idx = numpy.argwhere(abs(s1) > 0.4)
for i, j in idx:
logger.debug(casscf,
'Init guess <mo-CAS|mo-hf> %d %d %12.8f',
ncore + i + 1, j + 1, s1[i, j])
return mo
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
xmol, contr_coeff = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert('1E' in self.approx.upper())
t = xmol.intor_symmetric('cint1e_kin_sph')
v = xmol.intor_symmetric('cint1e_nuc_sph')
s = xmol.intor_symmetric('cint1e_ovlp_sph')
w = xmol.intor_symmetric('cint1e_pnucp_sph')
if 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_nr_by_atom()
nao = xmol.nao_nr()
x = numpy.zeros((nao,nao))
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = xmol.intor('cint1e_kin_sph', shls_slice=shls_slice)
v1 = xmol.intor('cint1e_nuc_sph', shls_slice=shls_slice)
s1 = xmol.intor('cint1e_ovlp_sph', shls_slice=shls_slice)
w1 = xmol.intor('cint1e_pnucp_sph', shls_slice=shls_slice)
x[p0:p1,p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('cint1e_ovlp_sph')
s21 = mole.intor_cross('cint1e_ovlp_sph', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
h1 = reduce(numpy.dot, (contr_coeff.T, h1, contr_coeff))
return h1
def symmetrize_orb(mol, mo, orbsym=None, s=None,
check=getattr(__config__, 'symm_addons_symmetrize_orb_check', False)):
'''Symmetrize the given orbitals.
This function is different to the :func:`symmetrize_space`: In this
function, each orbital is symmetrized by removing non-symmetric components.
:func:`symmetrize_space` symmetrizes the entire space by mixing different
orbitals.
Note this function might return non-orthorgonal orbitals.
Call :func:`symmetrize_space` to find the symmetrized orbitals that are
close to the given orbitals.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
orbsym : integer list
Irrep id for each orbital. If not given, the irreps are guessed
by calling :func:`label_orb_symm`.
s : 2D float array
Overlap matrix. If given, use this overlap than the the overlap
of the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_orb(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'B1', 'B2', 'B3', 'A', 'B1', 'B2', 'B3']
'''
if s is None:
s = mol.intor_symmetric('int1e_ovlp')
if orbsym is None:
orbsym = label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo, s=s, check=check)
orbsym = numpy.asarray(orbsym)
s_mo = numpy.dot(s, mo)
mo1 = numpy.empty_like(mo)
if orbsym[0] in mol.irrep_name:
irrep_id = mol.irrep_name
else:
irrep_id = mol.irrep_id
for i, ir in enumerate(irrep_id):
idx = orbsym == ir
csym = mol.symm_orb[i]
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
sc = lib.cho_solve(ovlpso, numpy.dot(csym.T, s_mo[:,idx]))
mo1[:,idx] = numpy.dot(csym, sc)
return mo1
def picture_change(self, even_operator=(None, None), odd_operator=None):
'''Picture change for even_operator + odd_operator
even_operator has two terms at diagonal blocks
[ v 0 ]
[ 0 w ]
odd_operator has the term at off-diagonal blocks
[ 0 p ]
[ p^T 0 ]
v, w, and p can be strings (integral name) or matrices.
'''
mol = self.mol
xmol, c = self.get_xmol(mol)
pc_mat = self._picture_change(xmol, even_operator, odd_operator)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp')
s21 = gto.mole.intor_cross('int1e_ovlp', xmol, mol)
c = lib.cho_solve(s22, s21)
elif self.xuncontract:
pass
else:
return pc_mat
if pc_mat.ndim == 2:
return lib.einsum('pi,pq,qj->ij', c, pc_mat, c)
else:
return lib.einsum('pi,xpq,qj->xij', c, pc_mat, c)
def project_dm_nr2nr(mol1, dm1, mol2):
r''' Project density matrix representation from basis set 1 (mol1) to basis
set 2 (mol2).
.. math::
|AO2\rangle DM_AO2 \langle AO2|
= |AO2\rangle P DM_AO1 P \langle AO2|
DM_AO2 = P DM_AO1 P
P = S_{AO2}^{-1}\langle AO2|AO1\rangle
There are three relevant functions:
:func:`project_dm_nr2nr` is the projection for non-relativistic (scalar) basis.
:func:`project_dm_nr2r` projects from non-relativistic to relativistic basis.
:func:`project_dm_r2r` is the projection between relativistic (spinor) basis.
'''
s22 = mol2.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', mol2, mol1)
p21 = lib.cho_solve(s22, s21)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def symmetrize_orb(mol, mo, orbsym=None, s=None,
check=getattr(__config__, 'symm_addons_symmetrize_orb_check', False)):
'''Symmetrize the given orbitals.
This function is different to the :func:`symmetrize_space`: In this
function, each orbital is symmetrized by removing non-symmetric components.
:func:`symmetrize_space` symmetrizes the entire space by mixing different
orbitals.
Note this function might return non-orthorgonal orbitals.
Call :func:`symmetrize_space` to find the symmetrized orbitals that are
close to the given orbitals.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
orbsym : integer list
Irrep id for each orbital. If not given, the irreps are guessed
by calling :func:`label_orb_symm`.
s : 2D float array
Overlap matrix. If given, use this overlap than the the overlap
of the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_orb(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'B1', 'B2', 'B3', 'A', 'B1', 'B2', 'B3']
'''
if s is None:
s = mol.intor_symmetric('int1e_ovlp')
if orbsym is None:
orbsym = label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo, s=s, check=check)
orbsym = numpy.asarray(orbsym)
s_mo = numpy.dot(s, mo)
mo1 = numpy.empty_like(mo)
if orbsym[0] in mol.irrep_name:
irrep_id = mol.irrep_name
else:
irrep_id = mol.irrep_id
for i, ir in enumerate(irrep_id):
idx = orbsym == ir
csym = mol.symm_orb[i]
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
sc = lib.cho_solve(ovlpso, numpy.dot(csym.T, s_mo[:,idx]))
mo1[:,idx] = numpy.dot(csym, sc)
return mo1
def picture_change(self, even_operator=(None, None), odd_operator=None):
'''Picture change for even_operator + odd_operator
even_operator has two terms at diagonal blocks
[ v 0 ]
[ 0 w ]
odd_operator has the term at off-diagonal blocks
[ 0 p ]
[ p^T 0 ]
v, w, and p can be strings (integral name) or matrices.
'''
mol = self.mol
xmol, contr_coeff_nr = self.get_xmol(mol)
pc_mat = self._picture_change(xmol, even_operator, odd_operator)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', xmol, mol)
c = lib.cho_solve(s22, s21)
elif self.xuncontract:
np, nc = contr_coeff_nr.shape
c = numpy.zeros((np * 2, nc * 2))
c[0::2, 0::2] = contr_coeff_nr
c[1::2, 1::2] = contr_coeff_nr
else:
return pc_mat
if pc_mat.ndim == 2:
return lib.einsum('pi,pq,qj->ij', c.conj(), pc_mat, c)
else:
return lib.einsum('pi,xpq,qj->xij', c.conj(), pc_mat, c)
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
xmol, contr_coeff = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
t = xmol.intor_symmetric('cint1e_kin_sph')
v = xmol.intor_symmetric('cint1e_nuc_sph')
s = xmol.intor_symmetric('cint1e_ovlp_sph')
w = xmol.intor_symmetric('cint1e_pnucp_sph')
if 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_nr_by_atom()
nao = xmol.nao_nr()
x = numpy.zeros((nao, nao))
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = xmol.intor('cint1e_kin_sph', shls_slice=shls_slice)
v1 = xmol.intor('cint1e_nuc_sph', shls_slice=shls_slice)
s1 = xmol.intor('cint1e_ovlp_sph', shls_slice=shls_slice)
w1 = xmol.intor('cint1e_pnucp_sph', shls_slice=shls_slice)
x[p0:p1, p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('cint1e_ovlp_sph')
s21 = mole.intor_cross('cint1e_ovlp_sph', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
h1 = reduce(numpy.dot, (contr_coeff.T, h1, contr_coeff))
return h1
def build_Lpq_nonpbc(mydf, auxcell):
if mydf.metric.upper() == 'S':
j3c = pyscf.df.incore.aux_e2(mydf.cell,
auxcell,
'cint3c1e_sph',
aosym='s2ij')
j2c = auxcell.intor_symmetric('cint1e_ovlp_sph')
else: # mydf.metric.upper() == 'T'
j3c = pyscf.df.incore.aux_e2(mydf.cell,
auxcell,
'cint3c1e_p2_sph',
aosym='s2ij')
j2c = auxcell.intor_symmetric('cint1e_kin_sph') * 2
naux = auxcell.nao_nr()
nao = mydf.cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
with h5py.File(mydf._cderi) as feri:
if 'Lpq' in feri:
del (feri['Lpq'])
chunks = (min(mydf.blockdim, naux), min(mydf.blockdim,
nao_pair)) # 512K
Lpq = feri.create_dataset('Lpq/0', (naux, nao_pair),
'f8',
chunks=chunks)
Lpq[:] = lib.cho_solve(j2c, j3c.T)
def project(mfmo, init_mo, ncore, s):
s_init_mo = numpy.einsum('pi,pi->i', init_mo.conj(), s.dot(init_mo))
if abs(s_init_mo - 1).max() < 1e-7 and mfmo.shape[1] == init_mo.shape[1]:
# Initial guess orbitals are orthonormal
return init_mo
# TODO: test whether the canonicalized orbitals are better than the projected orbitals
# Be careful that the ordering of the canonicalized orbitals may be very different
# to the CASSCF orbitals.
# else:
# fock = casscf.get_fock(mc, init_mo, casscf.ci)
# return casscf._scf.eig(fock, s)[1]
nocc = ncore + casscf.ncas
if ncore > 0:
mo0core = init_mo[:,:ncore]
s1 = reduce(numpy.dot, (mfmo.T, s, mo0core))
s1core = reduce(numpy.dot, (mo0core.T, s, mo0core))
coreocc = numpy.einsum('ij,ji->i', s1, lib.cho_solve(s1core, s1.T))
coreidx = numpy.sort(numpy.argsort(-coreocc)[:ncore])
logger.debug(casscf, 'Core indices %s', coreidx)
logger.debug(casscf, 'Core components %s', coreocc[coreidx])
# take HF core
mocore = mfmo[:,coreidx]
# take projected CAS space
mocas = init_mo[:,ncore:nocc] \
- reduce(numpy.dot, (mocore, mocore.T, s, init_mo[:,ncore:nocc]))
mocc = lo.orth.vec_lowdin(numpy.hstack((mocore, mocas)), s)
else:
mocc = lo.orth.vec_lowdin(init_mo[:,:nocc], s)
# remove core and active space from rest
if mocc.shape[1] < mfmo.shape[1]:
if casscf.mol.symmetry:
restorb = []
orbsym = scf.hf_symm.get_orbsym(casscf.mol, mfmo, s)
for ir in set(orbsym):
mo_ir = mfmo[:,orbsym==ir]
rest = mo_ir - reduce(numpy.dot, (mocc, mocc.T, s, mo_ir))
e, u = numpy.linalg.eigh(reduce(numpy.dot, (rest.T, s, rest)))
restorb.append(numpy.dot(rest, u[:,e>1e-7]))
restorb = numpy.hstack(restorb)
else:
rest = mfmo - reduce(numpy.dot, (mocc, mocc.T, s, mfmo))
e, u = numpy.linalg.eigh(reduce(numpy.dot, (rest.T, s, rest)))
restorb = numpy.dot(rest, u[:,e>1e-7])
mo = numpy.hstack((mocc, restorb))
else:
mo = mocc
if casscf.verbose >= logger.DEBUG:
s1 = reduce(numpy.dot, (mo[:,ncore:nocc].T, s, mfmo))
idx = numpy.argwhere(abs(s1) > 0.4)
for i,j in idx:
logger.debug(casscf, 'Init guess <mo-CAS|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s1[i,j])
return mo
def get_hcore(self, cell=None, kpts=None):
if cell is None: cell = self.cell
if kpts is None:
kpts_lst = numpy.zeros((1,3))
else:
kpts_lst = numpy.reshape(kpts, (-1,3))
xcell, contr_coeff = self.get_xmol(cell)
with_df = aft.AFTDF(xcell)
c = lib.param.LIGHT_SPEED
assert('1E' in self.approx.upper())
if 'ATOM' in self.approx.upper():
atom_slices = xcell.offset_nr_by_atom()
nao = xcell.nao_nr()
x = numpy.zeros((nao,nao))
vloc = numpy.zeros((nao,nao))
wloc = numpy.zeros((nao,nao))
for ia in range(xcell.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = xcell.intor('int1e_kin', shls_slice=shls_slice)
s1 = xcell.intor('int1e_ovlp', shls_slice=shls_slice)
with xcell.with_rinv_as_nucleus(ia):
z = -xcell.atom_charge(ia)
v1 = z * xcell.intor('int1e_rinv', shls_slice=shls_slice)
w1 = z * xcell.intor('int1e_prinvp', shls_slice=shls_slice)
vloc[p0:p1,p0:p1] = v1
wloc[p0:p1,p0:p1] = w1
x[p0:p1,p0:p1] = x2c._x2c1e_xmatrix(t1, v1, w1, s1, c)
else:
raise NotImplementedError
t = xcell.pbc_intor('int1e_kin', 1, lib.HERMITIAN, kpts_lst)
s = xcell.pbc_intor('int1e_ovlp', 1, lib.HERMITIAN, kpts_lst)
v = with_df.get_nuc(kpts_lst)
#w = get_pnucp(with_df, kpts_lst)
if self.basis is not None:
s22 = s
s21 = pbcgto.intor_cross('int1e_ovlp', xcell, cell, kpts=kpts_lst)
h1_kpts = []
for k in range(len(kpts_lst)):
# The treatment of pnucp local part has huge effects to hcore
#h1 = x2c._get_hcore_fw(t[k], vloc, wloc, s[k], x, c) - vloc + v[k]
#h1 = x2c._get_hcore_fw(t[k], v[k], w[k], s[k], x, c)
h1 = x2c._get_hcore_fw(t[k], v[k], wloc, s[k], x, c)
if self.basis is not None:
c = lib.cho_solve(s22[k], s21[k])
h1 = reduce(numpy.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
h1 = reduce(numpy.dot, (contr_coeff.T, h1, contr_coeff))
h1_kpts.append(h1)
if kpts is None or numpy.shape(kpts) == (3,):
h1_kpts = h1_kpts[0]
return lib.asarray(h1_kpts)
def get_hcore(self, cell=None, kpts=None):
if cell is None: cell = self.cell
if kpts is None:
kpts_lst = numpy.zeros((1, 3))
else:
kpts_lst = numpy.reshape(kpts, (-1, 3))
xcell, contr_coeff = self.get_xmol(cell)
with_df = aft.AFTDF(xcell)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
if 'ATOM' in self.approx.upper():
atom_slices = xcell.offset_nr_by_atom()
nao = xcell.nao_nr()
x = numpy.zeros((nao, nao))
vloc = numpy.zeros((nao, nao))
wloc = numpy.zeros((nao, nao))
for ia in range(xcell.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = xcell.intor('int1e_kin', shls_slice=shls_slice)
s1 = xcell.intor('int1e_ovlp', shls_slice=shls_slice)
with xcell.with_rinv_at_nucleus(ia):
z = -xcell.atom_charge(ia)
v1 = z * xcell.intor('int1e_rinv', shls_slice=shls_slice)
w1 = z * xcell.intor('int1e_prinvp', shls_slice=shls_slice)
vloc[p0:p1, p0:p1] = v1
wloc[p0:p1, p0:p1] = w1
x[p0:p1, p0:p1] = x2c._x2c1e_xmatrix(t1, v1, w1, s1, c)
else:
raise NotImplementedError
t = xcell.pbc_intor('int1e_kin', 1, lib.HERMITIAN, kpts_lst)
s = xcell.pbc_intor('int1e_ovlp', 1, lib.HERMITIAN, kpts_lst)
v = with_df.get_nuc(kpts_lst)
#w = get_pnucp(with_df, kpts_lst)
if self.basis is not None:
s22 = s
s21 = pbcgto.intor_cross('int1e_ovlp', xcell, cell, kpts=kpts_lst)
h1_kpts = []
for k in range(len(kpts_lst)):
# The treatment of pnucp local part has huge effects to hcore
#h1 = x2c._get_hcore_fw(t[k], vloc, wloc, s[k], x, c) - vloc + v[k]
#h1 = x2c._get_hcore_fw(t[k], v[k], w[k], s[k], x, c)
h1 = x2c._get_hcore_fw(t[k], v[k], wloc, s[k], x, c)
if self.basis is not None:
c = lib.cho_solve(s22[k], s21[k])
h1 = reduce(numpy.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
h1 = reduce(numpy.dot, (contr_coeff.T, h1, contr_coeff))
h1_kpts.append(h1)
if kpts is None or numpy.shape(kpts) == (3, ):
h1_kpts = h1_kpts[0]
return lib.asarray(h1_kpts)
def project_mo_nr2r(mol1, mo1, mol2):
s22 = mol2.intor_symmetric('cint1e_ovlp')
s21 = mole.intor_cross('cint1e_ovlp_sph', mol2, mol1)
ua, ub = symm.cg.real2spinor_whole(mol2)
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
mo2 = numpy.dot(s21, mo1)
return lib.cho_solve(s22, mo2)
def project_mo_nr2r(mol1, mo1, mol2):
s22 = mol2.intor_symmetric('cint1e_ovlp')
s21 = mole.intor_cross('cint1e_ovlp_sph', mol2, mol1)
ua, ub = symm.cg.real2spinor_whole(mol2)
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
mo2 = numpy.dot(s21, mo1)
return lib.cho_solve(s22, mo2)
def get_hcore(self, mol=None):
'''2-component X2c Foldy-Wouthuysen (FW) Hamiltonian (including
spin-free and spin-dependent terms) in the j-adapted spinor basis.
'''
if mol is None: mol = self.mol
if mol.has_ecp():
raise NotImplementedError
xmol, contr_coeff_nr = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
s = xmol.intor_symmetric('int1e_ovlp_spinor')
t = xmol.intor_symmetric('int1e_spsp_spinor') * .5
v = xmol.intor_symmetric('int1e_nuc_spinor')
w = xmol.intor_symmetric('int1e_spnucsp_spinor')
if 'get_xmat' in self.__dict__:
# If the get_xmat method is overwritten by user, build the X
# matrix with the external get_xmat method
x = self.get_xmat(xmol)
h1 = _get_hcore_fw(t, v, w, s, x, c)
elif 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_2c_by_atom()
n2c = xmol.nao_2c()
x = numpy.zeros((n2c, n2c), dtype=numpy.complex)
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
s1 = xmol.intor('int1e_ovlp_spinor', shls_slice=shls_slice)
t1 = xmol.intor('int1e_spsp_spinor',
shls_slice=shls_slice) * .5
with xmol.with_rinv_at_nucleus(ia):
z = -xmol.atom_charge(ia)
v1 = z * xmol.intor('int1e_rinv_spinor',
shls_slice=shls_slice)
w1 = z * xmol.intor('int1e_sprinvsp_spinor',
shls_slice=shls_slice)
x[p0:p1, p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T.conj(), h1, c))
elif self.xuncontract:
np, nc = contr_coeff_nr.shape
contr_coeff = numpy.zeros((np * 2, nc * 2))
contr_coeff[0::2, 0::2] = contr_coeff_nr
contr_coeff[1::2, 1::2] = contr_coeff_nr
h1 = reduce(numpy.dot, (contr_coeff.T.conj(), h1, contr_coeff))
return h1
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
if mol.has_ecp():
raise NotImplementedError
xmol, contr_coeff = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
t = _block_diag(xmol.intor_symmetric('int1e_kin'))
v = _block_diag(xmol.intor_symmetric('int1e_nuc'))
s = _block_diag(xmol.intor_symmetric('int1e_ovlp'))
w = _sigma_dot(xmol.intor('int1e_spnucsp'))
if 'get_xmat' in self.__dict__:
# If the get_xmat method is overwritten by user, build the X
# matrix with the external get_xmat method
x = self.get_xmat(xmol)
h1 = _get_hcore_fw(t, v, w, s, x, c)
elif 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_nr_by_atom()
# spin-orbital basis is twice the size of NR basis
atom_slices[:, 2:] *= 2
nao = xmol.nao_nr() * 2
x = numpy.zeros((nao, nao))
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = _block_diag(xmol.intor('int1e_kin',
shls_slice=shls_slice))
s1 = _block_diag(
xmol.intor('int1e_ovlp', shls_slice=shls_slice))
with xmol.with_rinv_at_nucleus(ia):
z = -xmol.atom_charge(ia)
v1 = _block_diag(
z * xmol.intor('int1e_rinv', shls_slice=shls_slice))
w1 = _sigma_dot(
z *
xmol.intor('int1e_sprinvsp', shls_slice=shls_slice))
x[p0:p1, p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', xmol, mol)
c = _block_diag(lib.cho_solve(s22, s21))
h1 = reduce(lib.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
contr_coeff = _block_diag(contr_coeff)
h1 = reduce(lib.dot, (contr_coeff.T, h1, contr_coeff))
return h1
def project_dm_nr2r(mol1, dm1, mol2):
assert(not mol1.cart)
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_sph', mol2, mol1)
ua, ub = mol2.sph2spinor_coeff()
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
p21 = lib.cho_solve(s22, s21, strict_sym_pos=False)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def project_mo_nr2nr(mol1, mo1, mol2):
r''' Project orbital coefficients
.. math::
|\psi1> = |AO1> C1
|\psi2> = P |\psi1> = |AO2>S^{-1}<AO2| AO1> C1 = |AO2> C2
C2 = S^{-1}<AO2|AO1> C1
'''
s22 = mol2.intor_symmetric('cint1e_ovlp_sph')
s21 = mole.intor_cross('cint1e_ovlp_sph', mol2, mol1)
return lib.cho_solve(s22, numpy.dot(s21, mo1))
def project_mo_nr2nr(mol1, mo1, mol2):
r''' Project orbital coefficients
.. math::
|\psi1> = |AO1> C1
|\psi2> = P |\psi1> = |AO2>S^{-1}<AO2| AO1> C1 = |AO2> C2
C2 = S^{-1}<AO2|AO1> C1
'''
s22 = mol2.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', mol2, mol1)
return lib.cho_solve(s22, numpy.dot(s21, mo1))
def project_mo_nr2nr(mol1, mo1, mol2):
r''' Project orbital coefficients from basis set 1 (C1 for mol1) to basis
set 2 (C2 for mol2).
.. math::
|\psi1\rangle = |AO1\rangle C1
|\psi2\rangle = P |\psi1\rangle = |AO2\rangle S^{-1}\langle AO2| AO1\rangle> C1 = |AO2\rangle> C2
C2 = S^{-1}\langle AO2|AO1\rangle C1
There are three relevant functions:
:func:`project_mo_nr2nr` is the projection for non-relativistic (scalar) basis.
:func:`project_mo_nr2r` projects from non-relativistic to relativistic basis.
:func:`project_mo_r2r` is the projection between relativistic (spinor) basis.
'''
s22 = mol2.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', mol2, mol1)
if isinstance(mo1, numpy.ndarray) and mo1.ndim == 2:
return lib.cho_solve(s22, numpy.dot(s21, mo1))
else:
return [lib.cho_solve(s22, numpy.dot(s21, x)) for x in mo1]
def project_dm_nr2r(mol1, dm1, mol2):
__doc__ = project_dm_nr2nr.__doc__
assert(not mol1.cart)
s22 = mol2.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_sph', mol2, mol1)
ua, ub = mol2.sph2spinor_coeff()
s21 = numpy.dot(ua.T.conj(), s21) + numpy.dot(ub.T.conj(), s21) # (*)
# mo2: alpha, beta have been summed in Eq. (*)
# so DM = mo2[:,:nocc] * 1 * mo2[:,:nocc].H
p21 = lib.cho_solve(s22, s21)
if isinstance(dm1, numpy.ndarray) and dm1.ndim == 2:
return reduce(numpy.dot, (p21, dm1, p21.conj().T))
else:
return lib.einsum('pi,nij,qj->npq', p21, dm1, p21.conj())
def get_hcore(self, mol=None):
'''1-component X2c Foldy-Wouthuysen (FW Hamiltonian (spin-free part only)
'''
if mol is None: mol = self.mol
if mol.has_ecp():
raise NotImplementedError
xmol, contr_coeff = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
t = xmol.intor_symmetric('int1e_kin')
v = xmol.intor_symmetric('int1e_nuc')
s = xmol.intor_symmetric('int1e_ovlp')
w = xmol.intor_symmetric('int1e_pnucp')
if 'get_xmat' in self.__dict__:
# If the get_xmat method is overwritten by user, build the X
# matrix with the external get_xmat method
x = self.get_xmat(xmol)
h1 = x2c._get_hcore_fw(t, v, w, s, x, c)
elif 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_nr_by_atom()
nao = xmol.nao_nr()
x = numpy.zeros((nao, nao))
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
t1 = xmol.intor('int1e_kin', shls_slice=shls_slice)
s1 = xmol.intor('int1e_ovlp', shls_slice=shls_slice)
with xmol.with_rinv_at_nucleus(ia):
z = -xmol.atom_charge(ia)
v1 = z * xmol.intor('int1e_rinv', shls_slice=shls_slice)
w1 = z * xmol.intor('int1e_prinvp', shls_slice=shls_slice)
x[p0:p1, p0:p1] = x2c._x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = x2c._get_hcore_fw(t, v, w, s, x, c)
else:
h1 = x2c._x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp')
s21 = gto.intor_cross('int1e_ovlp', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T, h1, c))
if self.xuncontract and contr_coeff is not None:
h1 = reduce(numpy.dot, (contr_coeff.T, h1, contr_coeff))
return h1
def build_Lpq_nonpbc(mydf, auxcell):
if mydf.metric.upper() == "S":
j3c = pyscf.df.incore.aux_e2(mydf.cell, auxcell, "cint3c1e_sph", aosym="s2ij")
j2c = auxcell.intor_symmetric("cint1e_ovlp_sph")
else: # mydf.metric.upper() == 'T'
j3c = pyscf.df.incore.aux_e2(mydf.cell, auxcell, "cint3c1e_p2_sph", aosym="s2ij")
j2c = auxcell.intor_symmetric("cint1e_kin_sph") * 2
naux = auxcell.nao_nr()
nao = mydf.cell.nao_nr()
nao_pair = nao * (nao + 1) // 2
with h5py.File(mydf._cderi) as feri:
if "Lpq" in feri:
del (feri["Lpq"])
chunks = (min(mydf.blockdim, naux), min(mydf.blockdim, nao_pair)) # 512K
Lpq = feri.create_dataset("Lpq/0", (naux, nao_pair), "f8", chunks=chunks)
Lpq[:] = lib.cho_solve(j2c, j3c.T)
def hcore_hess_generator(x2cobj, mol=None):
'''nuclear gradients of 1-component X2c hcore Hamiltonian (spin-free part only)
'''
if mol is None: mol = x2cobj.mol
xmol, contr_coeff = x2cobj.get_xmol(mol)
if x2cobj.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp')
s21 = gto.intor_cross('int1e_ovlp', xmol, mol)
contr_coeff = lib.cho_solve(s22, s21)
get_h1_xmol = gen_sf_hfw(xmol, x2cobj.approx)
def hcore_deriv(ia, ja):
h1 = get_h1_xmol(ia, ja)
if contr_coeff is not None:
h1 = lib.einsum('pi,xypq,qj->xyij', contr_coeff, h1, contr_coeff)
return numpy.asarray(h1)
return hcore_deriv
def build_Lpq_nonpbc(mydf, auxcell):
if mydf.metric.upper() == 'S':
j3c = pyscf.df.incore.aux_e2(mydf.cell, auxcell, 'cint3c1e_sph',
aosym='s2ij')
j2c = auxcell.intor_symmetric('cint1e_ovlp_sph')
else: # mydf.metric.upper() == 'T'
j3c = pyscf.df.incore.aux_e2(mydf.cell, auxcell, 'cint3c1e_p2_sph',
aosym='s2ij')
j2c = auxcell.intor_symmetric('cint1e_kin_sph') * 2
naux = auxcell.nao_nr()
nao = mydf.cell.nao_nr()
nao_pair = nao * (nao+1) // 2
with h5py.File(mydf._cderi) as feri:
if 'Lpq' in feri:
del(feri['Lpq'])
chunks = (min(mydf.blockdim,naux), min(mydf.blockdim,nao_pair)) # 512K
Lpq = feri.create_dataset('Lpq/0', (naux,nao_pair), 'f8', chunks=chunks)
Lpq[:] = lib.cho_solve(j2c, j3c.T)
def project(mfmo, init_mo, ncore, s):
nocc = ncore + casscf.ncas
if ncore > 0:
mo0core = init_mo[:, :ncore]
s1 = reduce(numpy.dot, (mfmo.T, s, mo0core))
s1core = reduce(numpy.dot, (mo0core.T, s, mo0core))
coreocc = numpy.einsum('ij,ji->i', s1, lib.cho_solve(s1core, s1.T))
coreidx = numpy.sort(numpy.argsort(-coreocc)[:ncore])
logger.debug(casscf, 'Core indices %s', coreidx)
logger.debug(casscf, 'Core components %s', coreocc[coreidx])
# take HF core
mocore = mfmo[:, coreidx]
# take projected CAS space
mocas = init_mo[:,ncore:nocc] \
- reduce(numpy.dot, (mocore, mocore.T, s, init_mo[:,ncore:nocc]))
mocc = lo.orth.vec_lowdin(numpy.hstack((mocore, mocas)), s)
else:
mocc = init_mo[:, :nocc]
# remove core and active space from rest
if mocc.shape[1] < mfmo.shape[1]:
rest = mfmo - reduce(numpy.dot, (mocc, mocc.T, s, mfmo))
e, u = numpy.linalg.eigh(reduce(numpy.dot, (rest.T, s, rest)))
restorb = numpy.dot(rest, u[:, e > 1e-7])
if casscf.mol.symmetry:
t = casscf.mol.intor_symmetric('int1e_kin')
t = reduce(numpy.dot, (restorb.T, t, restorb))
e, u = numpy.linalg.eigh(t)
restorb = numpy.dot(restorb, u)
mo = numpy.hstack((mocc, restorb))
else:
mo = mocc
if casscf.verbose >= logger.DEBUG:
s1 = reduce(numpy.dot, (mo[:, ncore:nocc].T, s, mfmo))
idx = numpy.argwhere(abs(s1) > 0.4)
for i, j in idx:
logger.debug(casscf,
'Init guess <mo-CAS|mo-hf> %d %d %12.8f',
ncore + i + 1, j + 1, s1[i, j])
return mo
def project(mfmo, init_mo, ncore, s):
nocc = ncore + casscf.ncas
if ncore > 0:
mo0core = init_mo[:,:ncore]
s1 = reduce(numpy.dot, (mfmo.T, s, mo0core))
s1core = reduce(numpy.dot, (mo0core.T, s, mo0core))
coreocc = numpy.einsum('ij,ji->i', s1, lib.cho_solve(s1core, s1.T))
coreidx = numpy.sort(numpy.argsort(-coreocc)[:ncore])
logger.debug(casscf, 'Core indices %s', coreidx)
logger.debug(casscf, 'Core components %s', coreocc[coreidx])
# take HF core
mocore = mfmo[:,coreidx]
# take projected CAS space
mocas = init_mo[:,ncore:nocc] \
- reduce(numpy.dot, (mocore, mocore.T, s, init_mo[:,ncore:nocc]))
mocc = lo.orth.vec_lowdin(numpy.hstack((mocore, mocas)), s)
else:
mocc = init_mo[:,:nocc]
# remove core and active space from rest
if mocc.shape[1] < mfmo.shape[1]:
rest = mfmo - reduce(numpy.dot, (mocc, mocc.T, s, mfmo))
e, u = numpy.linalg.eigh(reduce(numpy.dot, (rest.T, s, rest)))
restorb = numpy.dot(rest, u[:,e>1e-7])
if casscf.mol.symmetry:
t = casscf.mol.intor_symmetric('cint1e_kin_sph')
t = reduce(numpy.dot, (restorb.T, t, restorb))
e, u = numpy.linalg.eigh(t)
restorb = numpy.dot(restorb, u)
mo = numpy.hstack((mocc, restorb))
else:
mo = mocc
if casscf.verbose >= logger.DEBUG:
s1 = reduce(numpy.dot, (mo[:,ncore:nocc].T, s, mfmo))
idx = numpy.argwhere(abs(s1) > 0.4)
for i,j in idx:
logger.debug(casscf, 'Init guess <mo-CAS|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s1[i,j])
return mo
def get_hcore(self, mol=None):
'''2-component X2c hcore Hamiltonian (including spin-free and
spin-dependent terms) in the j-adapted spinor basis.
'''
if mol is None: mol = self.mol
xmol, contr_coeff_nr = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert ('1E' in self.approx.upper())
s = xmol.intor_symmetric('int1e_ovlp_spinor')
t = xmol.intor_symmetric('int1e_spsp_spinor') * .5
v = xmol.intor_symmetric('int1e_nuc_spinor')
w = xmol.intor_symmetric('int1e_spnucsp_spinor')
if 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_2c_by_atom()
n2c = xmol.nao_2c()
x = numpy.zeros((n2c, n2c), dtype=numpy.complex)
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
s1 = xmol.intor('int1e_ovlp_spinor', shls_slice=shls_slice)
t1 = xmol.intor('int1e_spsp_spinor',
shls_slice=shls_slice) * .5
v1 = xmol.intor('int1e_nuc_spinor', shls_slice=shls_slice)
w1 = xmol.intor('int1e_spnucsp_spinor', shls_slice=shls_slice)
x[p0:p1, p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp_spinor')
s21 = mole.intor_cross('int1e_ovlp_spinor', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T.conj(), h1, c))
elif self.xuncontract:
np, nc = contr_coeff_nr.shape
contr_coeff = numpy.zeros((np * 2, nc * 2))
contr_coeff[0::2, 0::2] = contr_coeff_nr
contr_coeff[1::2, 1::2] = contr_coeff_nr
h1 = reduce(numpy.dot, (contr_coeff.T.conj(), h1, contr_coeff))
return h1
def picture_change(self, even_operator=(None, None), odd_operator=None):
mol = self.mol
xmol, c = self.get_xmol(mol)
pc_mat = self._picture_change(xmol, even_operator, odd_operator)
if self.basis is not None:
s22 = xmol.intor_symmetric('int1e_ovlp')
s21 = mole.intor_cross('int1e_ovlp', xmol, mol)
c = lib.cho_solve(s22, s21)
elif self.xuncontract:
pass
else:
return pc_mat
c = _block_diag(c)
if pc_mat.ndim == 2:
return lib.einsum('pi,pq,qj->ij', c, pc_mat, c)
else:
return lib.einsum('pi,xpq,qj->xij', c, pc_mat, c)
def get_hcore(self, mol=None):
if mol is None: mol = self.mol
xmol, contr_coeff_nr = self.get_xmol(mol)
c = lib.param.LIGHT_SPEED
assert('1E' in self.approx.upper())
s = xmol.intor_symmetric('cint1e_ovlp')
t = xmol.intor_symmetric('cint1e_spsp') * .5
v = xmol.intor_symmetric('cint1e_nuc')
w = xmol.intor_symmetric('cint1e_spnucsp')
if 'ATOM' in self.approx.upper():
atom_slices = xmol.offset_2c_by_atom()
n2c = xmol.nao_2c()
x = numpy.zeros((n2c,n2c), dtype=numpy.complex)
for ia in range(xmol.natm):
ish0, ish1, p0, p1 = atom_slices[ia]
shls_slice = (ish0, ish1, ish0, ish1)
s1 = xmol.intor('cint1e_ovlp', shls_slice=shls_slice)
t1 = xmol.intor('cint1e_spsp', shls_slice=shls_slice) * .5
v1 = xmol.intor('cint1e_nuc', shls_slice=shls_slice)
w1 = xmol.intor('cint1e_spnucsp', shls_slice=shls_slice)
x[p0:p1,p0:p1] = _x2c1e_xmatrix(t1, v1, w1, s1, c)
h1 = _get_hcore_fw(t, v, w, s, x, c)
else:
h1 = _x2c1e_get_hcore(t, v, w, s, c)
if self.basis is not None:
s22 = xmol.intor_symmetric('cint1e_ovlp')
s21 = mole.intor_cross('cint1e_ovlp', xmol, mol)
c = lib.cho_solve(s22, s21)
h1 = reduce(numpy.dot, (c.T.conj(), h1, c))
elif self.xuncontract:
np, nc = contr_coeff_nr.shape
contr_coeff = numpy.zeros((np*2,nc*2))
contr_coeff[0::2,0::2] = contr_coeff_nr
contr_coeff[1::2,1::2] = contr_coeff_nr
h1 = reduce(numpy.dot, (contr_coeff.T.conj(), h1, contr_coeff))
return h1
def symmetrize_space(mol, mo, s=None, check=True):
'''Symmetrize the given orbital space.
This function is different to the :func:`symmetrize_orb`: In this function,
the given orbitals are mixed to reveal the symmtery; :func:`symmetrize_orb`
projects out non-symmetric components for each orbital.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
s : 2D float array
Overlap matrix. If not given, overlap is computed with the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_space(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'A', 'B1', 'B1', 'B2', 'B2', 'B3', 'B3']
'''
from pyscf.tools import mo_mapping
if s is None:
s = mol.intor_symmetric('cint1e_ovlp_sph')
nmo = mo.shape[1]
mo_s = numpy.dot(mo.T, s)
if check:
assert (numpy.allclose(numpy.dot(mo_s, mo), numpy.eye(nmo)))
mo1 = []
for i, csym in enumerate(mol.symm_orb):
moso = numpy.dot(mo_s, csym)
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
# excluding orbitals which are already symmetrized
try:
diag = numpy.einsum('ik,ki->i', moso,
lib.cho_solve(ovlpso, moso.T))
except:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
diag = numpy.einsum('ik,ki->i', moso,
lib.cho_solve(ovlpso, moso.T))
idx = abs(1 - diag) < 1e-8
orb_exclude = mo[:, idx]
mo1.append(orb_exclude)
moso1 = moso[~idx]
dm = numpy.dot(moso1.T, moso1)
if dm.trace() > 1e-8:
e, u = scipy.linalg.eigh(dm, ovlpso)
mo1.append(numpy.dot(csym, u[:, abs(1 - e) < 1e-6]))
mo1 = numpy.hstack(mo1)
if mo1.shape[1] != nmo:
raise ValueError('The input orbital space is not symmetrized.\n It is '
'probably because the input mol and orbitals are of '
'different orientation.')
snorm = numpy.linalg.norm(
reduce(numpy.dot, (mo1.T, s, mo1)) - numpy.eye(nmo))
if check and snorm > 1e-6:
raise ValueError('Orbitals are not orthogonalized')
idx = mo_mapping.mo_1to1map(reduce(numpy.dot, (mo.T, s, mo1)))
return mo1[:, idx]
def label_orb_symm(mol, irrep_name, symm_orb, mo, s=None, check=True, tol=1e-9):
"""Label the symmetry of given orbitals
irrep_name can be either the symbol or the ID of the irreducible
representation. If the ID is provided, it returns the numeric code
associated with XOR operator, see :py:meth:`symm.param.IRREP_ID_TABLE`
Args:
mol : an instance of :class:`Mole`
irrep_name : list of str or int
A list of irrep ID or name, it can be either mol.irrep_id or
mol.irrep_name. It can affect the return "label".
symm_orb : list of 2d array
the symmetry adapted basis
mo : 2d array
the orbitals to label
Returns:
list of symbols or integers to represent the irreps for the given
orbitals
Examples:
>>> from pyscf import gto, scf, symm
>>> mol = gto.M(atom='H 0 0 0; H 0 0 1', basis='ccpvdz',verbose=0, symmetry=1)
>>> mf = scf.RHF(mol)
>>> mf.kernel()
>>> symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mf.mo_coeff)
['Ag', 'B1u', 'Ag', 'B1u', 'B2u', 'B3u', 'Ag', 'B2g', 'B3g', 'B1u']
>>> symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mf.mo_coeff)
[0, 5, 0, 5, 6, 7, 0, 2, 3, 5]
"""
nmo = mo.shape[1]
if s is None:
s = mol.intor_symmetric("cint1e_ovlp_sph")
mo_s = numpy.dot(mo.T, s)
norm = numpy.zeros((len(irrep_name), nmo))
for i, csym in enumerate(symm_orb):
moso = numpy.dot(mo_s, csym)
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
try:
norm[i] = numpy.einsum("ik,ki->i", moso, lib.cho_solve(ovlpso, moso.T))
except:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
norm[i] = numpy.einsum("ik,ki->i", moso, lib.cho_solve(ovlpso, moso.T))
norm /= numpy.sum(norm, axis=0) # for orbitals which are not normalized
iridx = numpy.argmax(norm, axis=0)
orbsym = numpy.asarray([irrep_name[i] for i in iridx])
logger.debug(mol, "irreps of each MO %s", orbsym)
if check:
largest_norm = norm[iridx, numpy.arange(nmo)]
orbidx = numpy.where(largest_norm < 1 - tol)[0]
if orbidx.size > 0:
idx = numpy.where(largest_norm < 1 - tol * 1e2)[0]
if idx.size > 0:
raise ValueError("orbitals %s not symmetrized, norm = %s" % (idx, largest_norm[idx]))
else:
logger.warn(mol, "orbitals %s not strictly symmetrized.", numpy.unique(orbidx))
logger.warn(mol, "They can be symmetrized with " "pyscf.symm.symmetrize_space function.")
logger.debug(mol, "norm = %s", largest_norm[orbidx])
return orbsym
def symmetrize_space(mol, mo, s=None, check=True):
"""Symmetrize the given orbital space.
This function is different to the :func:`symmetrize_orb`: In this function,
the given orbitals are mixed to reveal the symmtery; :func:`symmetrize_orb`
projects out non-symmetric components for each orbital.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
s : 2D float array
Overlap matrix. If not given, overlap is computed with the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_space(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'A', 'B1', 'B1', 'B2', 'B2', 'B3', 'B3']
"""
from pyscf.tools import mo_mapping
if s is None:
s = mol.intor_symmetric("cint1e_ovlp_sph")
nmo = mo.shape[1]
mo_s = numpy.dot(mo.T, s)
if check:
assert numpy.allclose(numpy.dot(mo_s, mo), numpy.eye(nmo))
mo1 = []
for i, csym in enumerate(mol.symm_orb):
moso = numpy.dot(mo_s, csym)
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
# excluding orbitals which are already symmetrized
try:
diag = numpy.einsum("ik,ki->i", moso, lib.cho_solve(ovlpso, moso.T))
except:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
diag = numpy.einsum("ik,ki->i", moso, lib.cho_solve(ovlpso, moso.T))
idx = abs(1 - diag) < 1e-8
orb_exclude = mo[:, idx]
mo1.append(orb_exclude)
moso1 = moso[~idx]
dm = numpy.dot(moso1.T, moso1)
if dm.trace() > 1e-8:
e, u = scipy.linalg.eigh(dm, ovlpso)
mo1.append(numpy.dot(csym, u[:, abs(1 - e) < 1e-6]))
mo1 = numpy.hstack(mo1)
if mo1.shape[1] != nmo:
raise ValueError(
"The input orbital space is not symmetrized.\n It is "
"probably because the input mol and orbitals are of "
"different orientation."
)
snorm = numpy.linalg.norm(reduce(numpy.dot, (mo1.T, s, mo1)) - numpy.eye(nmo))
if check and snorm > 1e-6:
raise ValueError("Orbitals are not orthogonalized")
idx = mo_mapping.mo_1to1map(reduce(numpy.dot, (mo.T, s, mo1)))
return mo1[:, idx]
def symmetrize_space(mol,
mo,
s=None,
check=getattr(__config__,
'symm_addons_symmetrize_space_check', True),
tol=getattr(__config__,
'symm_addons_symmetrize_space_tol', 1e-7)):
'''Symmetrize the given orbital space.
This function is different to the :func:`symmetrize_orb`: In this function,
the given orbitals are mixed to reveal the symmtery; :func:`symmetrize_orb`
projects out non-symmetric components for each orbital.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
s : 2D float array
Overlap matrix. If not given, overlap is computed with the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_space(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'A', 'B1', 'B1', 'B2', 'B2', 'B3', 'B3']
'''
from pyscf.tools import mo_mapping
if s is None:
s = mol.intor_symmetric('int1e_ovlp')
nmo = mo.shape[1]
s_mo = numpy.dot(s, mo)
if check and abs(numpy.dot(mo.conj().T, s_mo) -
numpy.eye(nmo)).max() > tol:
raise ValueError('Orbitals are not orthogonalized')
mo1 = []
for i, csym in enumerate(mol.symm_orb):
moso = numpy.dot(csym.T.conj(), s_mo)
ovlpso = reduce(numpy.dot, (csym.T.conj(), s, csym))
# excluding orbitals which are already symmetrized
try:
diag = numpy.einsum('ki,ki->i', moso.conj(),
lib.cho_solve(ovlpso, moso))
except numpy.linalg.LinAlgError:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
diag = numpy.einsum('ki,ki->i', moso.conj(),
lib.cho_solve(ovlpso, moso))
idx = abs(1 - diag) < 1e-8
orb_exclude = mo[:, idx]
mo1.append(orb_exclude)
moso1 = moso[:, ~idx]
dm = numpy.dot(moso1, moso1.T.conj())
if dm.trace() > 1e-8:
e, u = scipy.linalg.eigh(dm, ovlpso)
mo1.append(numpy.dot(csym, u[:, abs(1 - e) < 1e-6]))
mo1 = numpy.hstack(mo1)
if mo1.shape[1] != nmo:
raise ValueError('The input orbital space is not symmetrized.\n One '
'possible reason is that the input mol and orbitals '
'are of different orientation.')
if (check and
abs(reduce(numpy.dot, (mo1.conj().T, s, mo1)) -
numpy.eye(nmo)).max() > tol):
raise ValueError('Orbitals are not orthogonalized')
idx = mo_mapping.mo_1to1map(reduce(numpy.dot, (mo.T.conj(), s, mo1)))
return mo1[:, idx]
def label_orb_symm(mol,
irrep_name,
symm_orb,
mo,
s=None,
check=True,
tol=1e-9):
'''Label the symmetry of given orbitals
irrep_name can be either the symbol or the ID of the irreducible
representation. If the ID is provided, it returns the numeric code
associated with XOR operator, see :py:meth:`symm.param.IRREP_ID_TABLE`
Args:
mol : an instance of :class:`Mole`
irrep_name : list of str or int
A list of irrep ID or name, it can be either mol.irrep_id or
mol.irrep_name. It can affect the return "label".
symm_orb : list of 2d array
the symmetry adapted basis
mo : 2d array
the orbitals to label
Returns:
list of symbols or integers to represent the irreps for the given
orbitals
Examples:
>>> from pyscf import gto, scf, symm
>>> mol = gto.M(atom='H 0 0 0; H 0 0 1', basis='ccpvdz',verbose=0, symmetry=1)
>>> mf = scf.RHF(mol)
>>> mf.kernel()
>>> symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mf.mo_coeff)
['Ag', 'B1u', 'Ag', 'B1u', 'B2u', 'B3u', 'Ag', 'B2g', 'B3g', 'B1u']
>>> symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mf.mo_coeff)
[0, 5, 0, 5, 6, 7, 0, 2, 3, 5]
'''
nmo = mo.shape[1]
if s is None:
s = mol.intor_symmetric('cint1e_ovlp_sph')
mo_s = numpy.dot(mo.T, s)
norm = numpy.zeros((len(irrep_name), nmo))
for i, csym in enumerate(symm_orb):
moso = numpy.dot(mo_s, csym)
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
try:
norm[i] = numpy.einsum('ik,ki->i', moso,
lib.cho_solve(ovlpso, moso.T))
except:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
norm[i] = numpy.einsum('ik,ki->i', moso,
lib.cho_solve(ovlpso, moso.T))
norm /= numpy.sum(norm, axis=0) # for orbitals which are not normalized
iridx = numpy.argmax(norm, axis=0)
orbsym = numpy.asarray([irrep_name[i] for i in iridx])
logger.debug(mol, 'irreps of each MO %s', orbsym)
if check:
largest_norm = norm[iridx, numpy.arange(nmo)]
orbidx = numpy.where(largest_norm < 1 - tol)[0]
if orbidx.size > 0:
idx = numpy.where(largest_norm < 1 - tol * 1e2)[0]
if idx.size > 0:
raise ValueError('orbitals %s not symmetrized, norm = %s' %
(idx, largest_norm[idx]))
else:
logger.warn(mol, 'orbitals %s not strictly symmetrized.',
numpy.unique(orbidx))
logger.warn(
mol, 'They can be symmetrized with '
'pyscf.symm.symmetrize_space function.')
logger.debug(mol, 'norm = %s', largest_norm[orbidx])
return orbsym
def symmetrize_space(mol, mo, s=None,
check=getattr(__config__, 'symm_addons_symmetrize_space_check', True),
tol=getattr(__config__, 'symm_addons_symmetrize_space_tol', 1e-7)):
'''Symmetrize the given orbital space.
This function is different to the :func:`symmetrize_orb`: In this function,
the given orbitals are mixed to reveal the symmtery; :func:`symmetrize_orb`
projects out non-symmetric components for each orbital.
Args:
mo : 2D float array
The orbital space to symmetrize
Kwargs:
s : 2D float array
Overlap matrix. If not given, overlap is computed with the input mol.
Returns:
2D orbital coefficients
Examples:
>>> from pyscf import gto, symm, scf
>>> mol = gto.M(atom = 'C 0 0 0; H 1 1 1; H -1 -1 1; H 1 -1 -1; H -1 1 -1',
... basis = 'sto3g')
>>> mf = scf.RHF(mol).run()
>>> mol.build(0, 0, symmetry='D2')
>>> mo = symm.symmetrize_space(mol, mf.mo_coeff)
>>> print(symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo))
['A', 'A', 'A', 'B1', 'B1', 'B2', 'B2', 'B3', 'B3']
'''
from pyscf.tools import mo_mapping
if s is None:
s = mol.intor_symmetric('int1e_ovlp')
nmo = mo.shape[1]
s_mo = numpy.dot(s, mo)
if check and abs(numpy.dot(mo.conj().T, s_mo) - numpy.eye(nmo)).max() > tol:
raise ValueError('Orbitals are not orthogonalized')
mo1 = []
for i, csym in enumerate(mol.symm_orb):
moso = numpy.dot(csym.T, s_mo)
ovlpso = reduce(numpy.dot, (csym.T, s, csym))
# excluding orbitals which are already symmetrized
try:
diag = numpy.einsum('ki,ki->i', moso.conj(), lib.cho_solve(ovlpso, moso))
except:
ovlpso[numpy.diag_indices(csym.shape[1])] += 1e-12
diag = numpy.einsum('ki,ki->i', moso.conj(), lib.cho_solve(ovlpso, moso))
idx = abs(1-diag) < 1e-8
orb_exclude = mo[:,idx]
mo1.append(orb_exclude)
moso1 = moso[:,~idx]
dm = numpy.dot(moso1, moso1.T.conj())
if dm.trace() > 1e-8:
e, u = scipy.linalg.eigh(dm, ovlpso)
mo1.append(numpy.dot(csym, u[:,abs(1-e) < 1e-6]))
mo1 = numpy.hstack(mo1)
if mo1.shape[1] != nmo:
raise ValueError('The input orbital space is not symmetrized.\n One '
'possible reason is that the input mol and orbitals '
'are of different orientation.')
if (check and
abs(reduce(numpy.dot, (mo1.conj().T, s, mo1)) - numpy.eye(nmo)).max() > tol):
raise ValueError('Orbitals are not orthogonalized')
idx = mo_mapping.mo_1to1map(reduce(numpy.dot, (mo.T, s, mo1)))
return mo1[:,idx]