def test_orth_ao(self):
c0 = orth.pre_orth_ao(mol, method='scf')
self.assertAlmostEqual(numpy.linalg.norm(c0), 5.7742626195362039, 9)
self.assertAlmostEqual(abs(c0).sum(), 33.461490657433551, 8)
c = orth.orth_ao(mol, 'lowdin', c0)
self.assertAlmostEqual(numpy.linalg.norm(c), 8.9823854843222257, 9)
self.assertAlmostEqual(abs(c).sum(), 94.933979307106767, 8)
c = orth.orth_ao(mol, 'meta_lowdin', c0)
self.assertAlmostEqual(numpy.linalg.norm(c), 8.9823854843222257, 9)
self.assertAlmostEqual(abs(c).sum(), 93.029386338534394, 8)
def test_orth_ao(self):
c0 = orth.pre_orth_ao(mol, method='scf')
self.assertAlmostEqual(numpy.linalg.norm(c0), 7.2617698799320358, 9)
self.assertAlmostEqual(abs(c0).sum(), 40.116080631662804, 8)
c = orth.orth_ao(mol, 'lowdin', c0)
self.assertAlmostEqual(numpy.linalg.norm(c), 10.967144073462256, 9)
self.assertAlmostEqual(abs(c).sum(), 112.23459140302003, 8)
c = orth.orth_ao(mol, 'meta_lowdin', c0)
self.assertAlmostEqual(numpy.linalg.norm(c), 10.967144073462256, 9)
self.assertAlmostEqual(abs(c).sum(), 111.61017124719302, 8)
def analyze(mf, verbose=logger.DEBUG, **kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mf.stdout, verbose)
log.note('**** MO energy ****')
if mf._focka_ao is None:
for i,c in enumerate(mo_occ):
log.note('MO #%-3d energy= %-18.15g occ= %g', i+1, mo_energy[i], c)
else:
mo_ea = numpy.einsum('ik,ik->k', mo_coeff, mf._focka_ao.dot(mo_coeff))
mo_eb = numpy.einsum('ik,ik->k', mo_coeff, mf._fockb_ao.dot(mo_coeff))
log.note(' Roothaan | alpha | beta')
for i,c in enumerate(mo_occ):
log.note('MO #%-3d energy= %-18.15g | %-18.15g | %-18.15g occ= %g',
i+1, mo_energy[i], mo_ea[i], mo_eb[i], c)
ovlp_ao = mf.get_ovlp()
if verbose >= logger.DEBUG:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
label = mf.mol.spheric_labels(True)
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(mf.stdout, c, label, start=1, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mf.mol, dm, s=s, verbose=log)
def analyze(mf, verbose=logger.DEBUG):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis; Diople moment.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mf.stdout, verbose)
log.note('**** MO energy ****')
for i,c in enumerate(mo_occ):
log.note('MO #%-3d energy= %-18.15g occ= %g', i+1, mo_energy[i], c)
ovlp_ao = mf.get_ovlp()
if verbose >= logger.DEBUG:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
label = mf.mol.spheric_labels(True)
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(mf.stdout, c, label, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return (mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
def mulliken_meta(cell, dm_ao_kpts, verbose=logger.DEBUG,
pre_orth_method=PRE_ORTH_METHOD, s=None):
'''A modified Mulliken population analysis, based on meta-Lowdin AOs.
Note this function only computes the Mulliken population for the gamma
point density matrix.
'''
from pyscf.lo import orth
if s is None:
s = khf.get_ovlp(cell)
log = logger.new_logger(cell, verbose)
log.note('Analyze output for *gamma point*.')
log.info(' To include the contributions from k-points, transform to a '
'supercell then run the population analysis on the supercell\n'
' from pyscf.pbc.tools import k2gamma\n'
' k2gamma.k2gamma(mf).mulliken_meta()')
log.note("KUHF mulliken_meta")
dm_ao_gamma = dm_ao_kpts[:,0,:,:].real
s_gamma = s[0,:,:].real
c = orth.restore_ao_character(cell, pre_orth_method)
orth_coeff = orth.orth_ao(cell, 'meta_lowdin', pre_orth_ao=c, s=s_gamma)
c_inv = np.dot(orth_coeff.T, s_gamma)
dm_a = reduce(np.dot, (c_inv, dm_ao_gamma[0], c_inv.T.conj()))
dm_b = reduce(np.dot, (c_inv, dm_ao_gamma[1], c_inv.T.conj()))
log.note(' ** Mulliken pop alpha/beta on meta-lowdin orthogonal AOs **')
return mol_uhf.mulliken_pop(cell, (dm_a,dm_b), np.eye(orth_coeff.shape[0]), log)
def atomic_init_guess(mol, mo_coeff):
s = mol.intor_symmetric('int1e_ovlp')
c = orth.orth_ao(mol, s=s)
mo = reduce(numpy.dot, (c.conj().T, s, mo_coeff))
nmo = mo_coeff.shape[1]
# Find the AOs which have largest overlap to MOs
idx = numpy.argsort(numpy.einsum('pi,pi->p', mo.conj(), mo))
nmo = mo.shape[1]
idx = idx[-nmo:]
u, w, vh = numpy.linalg.svd(mo[idx])
return lib.dot(vh, u.conj().T)
def test_ghost_atm_meta_lowdin(self):
mol = gto.Mole()
mol.atom = [["O" , (0. , 0. , 0.)],
['ghost' , (0. , -0.757, 0.587)],
[1 , (0. , 0.757 , 0.587)] ]
mol.spin = 1
mol.basis = {'O':'ccpvdz', 'H':'ccpvdz',
'GHOST': gto.basis.load('631g','H')}
mol.build()
c = orth.orth_ao(mol, method='meta_lowdin')
self.assertAlmostEqual(numpy.linalg.norm(c), 7.9067188905237256, 9)
def analyze(mf, verbose=logger.DEBUG, **kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Occupancy for each irreps; Mulliken population analysis
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mol = mf.mol
if not mol.symmetry:
return hf.analyze(mf, verbose, **kwargs)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
log = logger.Logger(mf.stdout, verbose)
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsym = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mo_coeff,
s=ovlp_ao, check=False)
orbsym = numpy.array(orbsym)
wfnsym = 0
noccs = [sum(orbsym[mo_occ>0]==ir) for ir in mol.irrep_id]
log.note('total symmetry = %s', symm.irrep_id2name(mol.groupname, wfnsym))
log.note('occupancy for each irrep: ' + (' %4s'*nirrep), *mol.irrep_name)
log.note('double occ ' + (' %4d'*nirrep), *noccs)
log.note('**** MO energy ****')
irname_full = {}
for k,ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%d (%s #%d), energy= %.15g occ= %g',
k+1, irname_full[j], irorbcnt[j], mo_energy[k], mo_occ[k])
if verbose >= logger.DEBUG:
label = mol.spheric_labels(True)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(mf.stdout, c, label, molabel, start=1, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
def atomic_init_guess(mol, mo_coeff):
s = mol.intor_symmetric('int1e_ovlp')
c = orth.orth_ao(mol, s=s)
mo = reduce(numpy.dot, (c.conj().T, s, mo_coeff))
# Find the AOs which have largest overlap to MOs
idx = numpy.argsort(numpy.einsum('pi,pi->p', mo.conj(), mo))
nmo = mo.shape[1]
idx = sorted(idx[-nmo:])
# Rotate mo_coeff, make it as close as possible to AOs
u, w, vh = numpy.linalg.svd(mo[idx])
return lib.dot(u, vh).conj().T
def analyze(mf, verbose=logger.DEBUG, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis; Dipole moment
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
nmo = len(mo_occ[0])
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
log.note('**** MO energy ****')
log.note(' alpha | beta alpha | beta')
for i in range(nmo):
log.note('MO #%-3d energy= %-18.15g | %-18.15g occ= %g | %g',
i+MO_BASE, mo_energy[0][i], mo_energy[1][i],
mo_occ[0][i], mo_occ[1][i])
ovlp_ao = mf.get_ovlp()
if log.verbose >= logger.DEBUG:
label = mf.mol.ao_labels()
if with_meta_lowdin:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) for alpha spin **')
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
dump_mat.dump_rec(mf.stdout, c_inv.dot(mo_coeff[0]), label,
start=MO_BASE, **kwargs)
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) for beta spin **')
dump_mat.dump_rec(mf.stdout, c_inv.dot(mo_coeff[1]), label,
start=MO_BASE, **kwargs)
else:
log.debug(' ** MO coefficients (expansion on AOs) for alpha spin **')
dump_mat.dump_rec(mf.stdout, mo_coeff[0], label,
start=MO_BASE, **kwargs)
log.debug(' ** MO coefficients (expansion on AOs) for beta spin **')
dump_mat.dump_rec(mf.stdout, mo_coeff[1], label,
start=MO_BASE, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
return (mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
else:
return (mf.mulliken_pop(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
def mulliken_meta(mol, dm_ao, verbose=logger.DEBUG,
pre_orth_method=PRE_ORTH_METHOD, s=None):
'''Mulliken population analysis, based on meta-Lowdin AOs.
'''
from pyscf.lo import orth
if s is None: s = hf.get_ovlp(mol)
log = logger.new_logger(mol, verbose)
if isinstance(dm_ao, numpy.ndarray) and dm_ao.ndim == 2:
dm_ao = numpy.array((dm_ao*.5, dm_ao*.5))
c = orth.restore_ao_character(mol, pre_orth_method)
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', pre_orth_ao=c, s=s)
c_inv = numpy.dot(orth_coeff.T, s)
dm_a = reduce(numpy.dot, (c_inv, dm_ao[0], c_inv.T.conj()))
dm_b = reduce(numpy.dot, (c_inv, dm_ao[1], c_inv.T.conj()))
log.note(' ** Mulliken pop alpha/beta on meta-lowdin orthogonal AOs **')
return mulliken_pop(mol, (dm_a,dm_b), numpy.eye(orth_coeff.shape[0]), log)
def mulliken_pop_meta_lowdin_ao(mol, dm_ao, verbose=logger.DEBUG,
pre_orth_method='ANO'):
'''Mulliken population analysis, based on meta-Lowdin AOs.
'''
from pyscf.lo import orth
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
c = orth.pre_orth_ao(mol, pre_orth_method)
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', pre_orth_ao=c)
c_inv = numpy.linalg.inv(orth_coeff)
dm_a = reduce(numpy.dot, (c_inv, dm_ao[0], c_inv.T.conj()))
dm_b = reduce(numpy.dot, (c_inv, dm_ao[1], c_inv.T.conj()))
log.info(' ** Mulliken pop alpha/beta on meta-lowdin orthogonal AOs **')
return mulliken_pop(mol, (dm_a,dm_b), numpy.eye(orth_coeff.shape[0]), log)
def analyze(mf, verbose=logger.DEBUG, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
log.note('**** MO energy ****')
if getattr(mo_energy, 'mo_ea', None) is not None:
mo_ea = mo_energy.mo_ea
mo_eb = mo_energy.mo_eb
log.note(' Roothaan | alpha | beta')
for i,c in enumerate(mo_occ):
log.note('MO #%-3d energy= %-18.15g | %-18.15g | %-18.15g occ= %g',
i+MO_BASE, mo_energy[i], mo_ea[i], mo_eb[i], c)
else:
for i,c in enumerate(mo_occ):
log.note('MO #%-3d energy= %-18.15g occ= %g',
i+MO_BASE, mo_energy[i], c)
ovlp_ao = mf.get_ovlp()
if log.verbose >= logger.DEBUG:
label = mf.mol.ao_labels()
if with_meta_lowdin:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
else:
log.debug(' ** MO coefficients (expansion on AOs) **')
c = mo_coeff
dump_mat.dump_rec(mf.stdout, c, label, start=MO_BASE, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
pop_and_charge = mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log)
else:
pop_and_charge = mf.mulliken_pop(mf.mol, dm, s=ovlp_ao, verbose=log)
dip = mf.dip_moment(mf.mol, dm, verbose=log)
return pop_and_charge, dip
def mulliken_meta(mol, dm, verbose=logger.DEBUG, pre_orth_method='ANO',
s=None):
'''Mulliken population analysis, based on meta-Lowdin AOs.
In the meta-lowdin, the AOs are grouped in three sets: core, valence and
Rydberg, the orthogonalization are carreid out within each subsets.
Args:
mol : an instance of :class:`Mole`
dm : ndarray or 2-item list of ndarray
Density matrix. ROHF dm is a 2-item list of 2D array
Kwargs:
verbose : int or instance of :class:`lib.logger.Logger`
pre_orth_method : str
Pre-orthogonalization, which localized GTOs for each atom.
To obtain the occupied and unoccupied atomic shells, there are
three methods
| 'ano' : Project GTOs to ANO basis
| 'minao' : Project GTOs to MINAO basis
| 'scf' : Fraction-averaged RHF
'''
from pyscf.lo import orth
if s is None:
s = get_ovlp(mol)
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
c = orth.pre_orth_ao(mol, pre_orth_method)
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', pre_orth_ao=c, s=s)
c_inv = numpy.dot(orth_coeff.T, s)
if isinstance(dm, numpy.ndarray) and dm.ndim == 2:
dm = reduce(numpy.dot, (c_inv, dm, c_inv.T.conj()))
else: # ROHF
dm = reduce(numpy.dot, (c_inv, dm[0]+dm[1], c_inv.T.conj()))
log.info(' ** Mulliken pop on meta-lowdin orthogonal AOs **')
return mulliken_pop(mol, dm, numpy.eye(orth_coeff.shape[0]), log)
def atomic_pops(mol, mo_coeff, method='meta_lowdin'):
'''kwarg method can be one of mulliken, lowdin, meta_lowdin
'''
s = mol.intor_symmetric('cint1e_ovlp_sph')
nmo = mo_coeff.shape[1]
proj = numpy.empty((mol.natm,nmo,nmo))
if method.lower() == 'mulliken':
for i, (b0, b1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
csc = reduce(numpy.dot, (mo_coeff[p0:p1].T, s[p0:p1], mo_coeff))
proj[i] = (csc + csc.T) * .5
elif method.lower() in ('lowdin', 'meta_lowdin'):
csc = reduce(numpy.dot, (mo_coeff.T, s, orth.orth_ao(mol, method, s=s)))
for i, (b0, b1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
proj[i] = numpy.dot(csc[:,p0:p1], csc[:,p0:p1].T)
else:
raise KeyError('method = %s' % method)
return proj
def mulliken_meta(mol, dm_ao, verbose=logger.DEBUG, pre_orth_method="ANO", s=None):
"""Mulliken population analysis, based on meta-Lowdin AOs.
"""
from pyscf.lo import orth
if s is None:
s = hf.get_ovlp(mol)
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
if isinstance(dm_ao, numpy.ndarray) and dm_ao.ndim == 2:
dm_ao = numpy.array((dm_ao * 0.5, dm_ao * 0.5))
c = orth.pre_orth_ao(mol, pre_orth_method)
orth_coeff = orth.orth_ao(mol, "meta_lowdin", pre_orth_ao=c, s=s)
c_inv = numpy.dot(orth_coeff.T, s)
dm_a = reduce(numpy.dot, (c_inv, dm_ao[0], c_inv.T.conj()))
dm_b = reduce(numpy.dot, (c_inv, dm_ao[1], c_inv.T.conj()))
log.info(" ** Mulliken pop alpha/beta on meta-lowdin orthogonal AOs **")
return mulliken_pop(mol, (dm_a, dm_b), numpy.eye(orth_coeff.shape[0]), log)
def analyze(mf, verbose=logger.DEBUG, **kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis; Dipole moment
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mf.stdout, verbose)
ss, s = mf.spin_square((mo_coeff[0][:,mo_occ[0]>0],
mo_coeff[1][:,mo_occ[1]>0]), mf.get_ovlp())
log.note('multiplicity <S^2> = %.8g 2S+1 = %.8g', ss, s)
log.note('**** MO energy ****')
log.note(' alpha | beta alpha | beta')
for i in range(mo_occ.shape[1]):
log.note('MO #%-3d energy= %-18.15g | %-18.15g occ= %g | %g',
i+1, mo_energy[0][i], mo_energy[1][i],
mo_occ[0][i], mo_occ[1][i])
ovlp_ao = mf.get_ovlp()
if verbose >= logger.DEBUG:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) for alpha spin **')
label = mf.mol.spheric_labels(True)
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
dump_mat.dump_rec(mf.stdout, c_inv.dot(mo_coeff[0]), label, start=1,
**kwargs)
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) for beta spin **')
dump_mat.dump_rec(mf.stdout, c_inv.dot(mo_coeff[1]), label, start=1,
**kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return (mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
def analyze(self, mo_coeff=None, ci=None, verbose=None,
large_ci_tol=LARGE_CI_TOL, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
log = logger.new_logger(self, verbose)
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
mocore_a = mo_coeff[0][:,:ncore[0]]
mocas_a = mo_coeff[0][:,ncore[0]:ncore[0]+ncas]
mocore_b = mo_coeff[1][:,:ncore[1]]
mocas_b = mo_coeff[1][:,ncore[1]:ncore[1]+ncas]
label = self.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(self.fcisolver, addons.StateAverageFCISolver)):
log.warn('Mulitple states found in UCASCI solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
casdm1a, casdm1b = self.fcisolver.make_rdm1s(civec, ncas, nelecas)
dm1a = numpy.dot(mocore_a, mocore_a.T)
dm1a += reduce(numpy.dot, (mocas_a, casdm1a, mocas_a.T))
dm1b = numpy.dot(mocore_b, mocore_b.T)
dm1b += reduce(numpy.dot, (mocas_b, casdm1b, mocas_b.T))
if log.verbose >= logger.DEBUG2:
log.debug2('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.debug2('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
if log.verbose >= logger.INFO:
ovlp_ao = self._scf.get_ovlp()
occa, ucasa = self._eig(-casdm1a, ncore[0], ncore[0]+ncas)
occb, ucasb = self._eig(-casdm1b, ncore[1], ncore[1]+ncas)
log.info('Natural alpha-occupancy %s', str(-occa))
log.info('Natural beta-occupancy %s', str(-occb))
mocas_a = numpy.dot(mocas_a, ucasa)
mocas_b = numpy.dot(mocas_b, ucasb)
if with_meta_lowdin:
orth_coeff = orth.orth_ao(self.mol, 'meta_lowdin', s=ovlp_ao)
mocas_a = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_a))
mocas_b = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_b))
log.info('Natural alpha-orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_a, label, start=1, **kwargs)
log.info('Natural beta-orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_b, label, start=1, **kwargs)
else:
log.info('Natural alpha-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_a, label, start=1, **kwargs)
log.info('Natural beta-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas_b, label, start=1, **kwargs)
tol = getattr(__config__, 'mcscf_addons_map2hf_tol', 0.4)
s = reduce(numpy.dot, (mo_coeff[0].T, ovlp_ao, self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s)>tol)
for i,j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
s = reduce(numpy.dot, (mo_coeff[1].T, ovlp_ao, self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s)>tol)
for i,j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' % (i+1,j+1,s[i,j]))
if getattr(self.fcisolver, 'large_ci', None) and ci is not None:
log.info('\n** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, state in enumerate(ci):
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
res = self.fcisolver.large_ci(state, self.ncas, self.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = self.fcisolver.large_ci(ci, self.ncas, self.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
return dm1a, dm1b
def cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
casdm1=None, verbose=None, with_meta_lowdin=WITH_META_LOWDIN):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
accordingly
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy.
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
log = logger.new_logger(mc, verbose)
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
# orbital symmetry is reserved in this _eig call
occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
casorb_idx = numpy.argsort(occ.round(9), kind='mergesort')
occ = occ[casorb_idx]
ucas = ucas[:,casorb_idx]
occ = -occ
mo_occ = numpy.zeros(mo_coeff.shape[1])
mo_occ[:ncore] = 2
mo_occ[ncore:nocc] = occ
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:,ncore:nocc] = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
if getattr(mo_coeff, 'orbsym', None) is not None:
orbsym = numpy.copy(mo_coeff.orbsym)
if sort:
orbsym[ncore:nocc] = orbsym[ncore:nocc][casorb_idx]
mo_coeff1 = lib.tag_array(mo_coeff1, orbsym=orbsym)
fcivec = None
if getattr(mc.fcisolver, 'transform_ci_for_orbital_rotation', None):
if isinstance(ci, numpy.ndarray):
fcivec = mc.fcisolver.transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
elif (isinstance(ci, (list, tuple)) and
all(isinstance(x[0], numpy.ndarray) for x in ci)):
fcivec = [mc.fcisolver.transform_ci_for_orbital_rotation(x, ncas, nelecas, ucas)
for x in ci]
elif getattr(mc.fcisolver, 'states_transform_ci_for_orbital_rotation', None):
fcivec = mc.fcisolver.states_transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
if fcivec is None:
log.info('FCI vector not available, call CASCI to update wavefunction')
mocas = mo_coeff1[:,ncore:nocc]
hcore = mc.get_hcore()
dm_core = numpy.dot(mo_coeff1[:,:ncore]*2, mo_coeff1[:,:ncore].T)
ecore = mc.energy_nuc()
ecore+= numpy.einsum('ij,ji', hcore, dm_core)
h1eff = reduce(numpy.dot, (mocas.T, hcore, mocas))
if getattr(eris, 'ppaa', None) is not None:
ecore += eris.vhf_c[:ncore,:ncore].trace()
h1eff += reduce(numpy.dot, (ucas.T, eris.vhf_c[ncore:nocc,ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc,ncore:nocc,:,:], ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
if getattr(mc, 'with_df', None):
raise NotImplementedError('cas_natorb for DFCASCI/DFCASSCF')
corevhf = mc.get_veff(mc.mol, dm_core)
ecore += numpy.einsum('ij,ji', dm_core, corevhf) * .5
h1eff += reduce(numpy.dot, (mocas.T, corevhf, mocas))
aaaa = ao2mo.kernel(mc.mol, mocas)
# See label_symmetry_ function in casci_symm.py which initialize the
# orbital symmetry information in fcisolver. This orbital symmetry
# labels should be reordered to match the sorted active space orbitals.
if sort and getattr(mo_coeff1, 'orbsym', None) is not None:
mc.fcisolver.orbsym = mo_coeff1.orbsym[ncore:nocc]
max_memory = max(400, mc.max_memory-lib.current_memory()[0])
e, fcivec = mc.fcisolver.kernel(h1eff, aaaa, ncas, nelecas, ecore=ecore,
max_memory=max_memory, verbose=log)
log.debug('In Natural orbital, CASCI energy = %s', e)
if log.verbose >= logger.INFO:
ovlp_ao = mc._scf.get_ovlp()
# where_natorb gives the new locations of the natural orbitals
where_natorb = mo_1to1map(ucas)
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(occ))
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.ao_labels()
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff1[:,ncore:nocc]))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
label = mc.mol.ao_labels()
mo_cas = mo_coeff1[:,ncore:nocc]
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:,ncore:nocc].T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s[i,j])
return mo_coeff1, fcivec, mo_occ
def cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
casdm1=None, verbose=None, with_meta_lowdin=WITH_META_LOWDIN):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy.
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
log = logger.new_logger(mc, verbose)
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
# orbital symmetry is reserved in this _eig call
occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
casorb_idx = numpy.argsort(occ.round(9), kind='mergesort')
occ = occ[casorb_idx]
ucas = ucas[:,casorb_idx]
occ = -occ
mo_occ = numpy.zeros(mo_coeff.shape[1])
mo_occ[:ncore] = 2
mo_occ[ncore:nocc] = occ
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:,ncore:nocc] = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
if getattr(mo_coeff, 'orbsym', None) is not None:
orbsym = numpy.copy(mo_coeff.orbsym)
if sort:
orbsym[ncore:nocc] = orbsym[ncore:nocc][casorb_idx]
mo_coeff1 = lib.tag_array(mo_coeff1, orbsym=orbsym)
if isinstance(ci, numpy.ndarray):
fcivec = fci.addons.transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
elif isinstance(ci, (tuple, list)) and isinstance(ci[0], numpy.ndarray):
# for state-average eigenfunctions
fcivec = [fci.addons.transform_ci_for_orbital_rotation(x, ncas, nelecas, ucas)
for x in ci]
else:
log.info('FCI vector not available, call CASCI for wavefunction')
mocas = mo_coeff1[:,ncore:nocc]
hcore = mc.get_hcore()
dm_core = numpy.dot(mo_coeff1[:,:ncore]*2, mo_coeff1[:,:ncore].T)
ecore = mc.energy_nuc()
ecore+= numpy.einsum('ij,ji', hcore, dm_core)
h1eff = reduce(numpy.dot, (mocas.T, hcore, mocas))
if getattr(eris, 'ppaa', None) is not None:
ecore += eris.vhf_c[:ncore,:ncore].trace()
h1eff += reduce(numpy.dot, (ucas.T, eris.vhf_c[ncore:nocc,ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc,ncore:nocc,:,:], ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
if getattr(mc, 'with_df', None):
raise NotImplementedError('cas_natorb for DFCASCI/DFCASSCF')
corevhf = mc.get_veff(mc.mol, dm_core)
ecore += numpy.einsum('ij,ji', dm_core, corevhf) * .5
h1eff += reduce(numpy.dot, (mocas.T, corevhf, mocas))
aaaa = ao2mo.kernel(mc.mol, mocas)
# See label_symmetry_ function in casci_symm.py which initialize the
# orbital symmetry information in fcisolver. This orbital symmetry
# labels should be reordered to match the sorted active space orbitals.
if sort and getattr(mo_coeff1, 'orbsym', None) is not None:
mc.fcisolver.orbsym = mo_coeff1.orbsym[ncore:nocc]
max_memory = max(400, mc.max_memory-lib.current_memory()[0])
e, fcivec = mc.fcisolver.kernel(h1eff, aaaa, ncas, nelecas, ecore=ecore,
max_memory=max_memory, verbose=log)
log.debug('In Natural orbital, CASCI energy = %s', e)
if log.verbose >= logger.INFO:
ovlp_ao = mc._scf.get_ovlp()
# where_natorb gives the new locations of the natural orbitals
where_natorb = mo_1to1map(ucas)
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(occ))
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.ao_labels()
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff1[:,ncore:nocc]))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
label = mc.mol.ao_labels()
mo_cas = mo_coeff1[:,ncore:nocc]
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:,ncore:nocc].T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s[i,j])
return mo_coeff1, fcivec, mo_occ
def analyze(self,
mo_coeff=None,
ci=None,
verbose=None,
large_ci_tol=LARGE_CI_TOL,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = self.mo_coeff
if ci is None: ci = self.ci
log = logger.new_logger(self, verbose)
nelecas = self.nelecas
ncas = self.ncas
ncore = self.ncore
mocore_a = mo_coeff[0][:, :ncore[0]]
mocas_a = mo_coeff[0][:, ncore[0]:ncore[0] + ncas]
mocore_b = mo_coeff[1][:, :ncore[1]]
mocas_b = mo_coeff[1][:, ncore[1]:ncore[1] + ncas]
label = self.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(self.fcisolver, addons.StateAverageFCISolver)):
log.warn(
'Mulitple states found in UCASCI solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
casdm1a, casdm1b = self.fcisolver.make_rdm1s(civec, ncas, nelecas)
dm1a = numpy.dot(mocore_a, mocore_a.T)
dm1a += reduce(numpy.dot, (mocas_a, casdm1a, mocas_a.T))
dm1b = numpy.dot(mocore_b, mocore_b.T)
dm1b += reduce(numpy.dot, (mocas_b, casdm1b, mocas_b.T))
if log.verbose >= logger.DEBUG2:
log.debug2('alpha density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1a, label)
log.debug2('beta density matrix (on AO)')
dump_mat.dump_tri(self.stdout, dm1b, label)
if log.verbose >= logger.INFO:
ovlp_ao = self._scf.get_ovlp()
occa, ucasa = self._eig(-casdm1a, ncore[0], ncore[0] + ncas)
occb, ucasb = self._eig(-casdm1b, ncore[1], ncore[1] + ncas)
log.info('Natural alpha-occupancy %s', str(-occa))
log.info('Natural beta-occupancy %s', str(-occb))
mocas_a = numpy.dot(mocas_a, ucasa)
mocas_b = numpy.dot(mocas_b, ucasb)
if with_meta_lowdin:
orth_coeff = orth.orth_ao(self.mol, 'meta_lowdin', s=ovlp_ao)
mocas_a = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_a))
mocas_b = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas_b))
log.info(
'Natural alpha-orbital (expansion on meta-Lowdin AOs) in CAS space'
)
dump_mat.dump_rec(log.stdout,
mocas_a,
label,
start=1,
**kwargs)
log.info(
'Natural beta-orbital (expansion on meta-Lowdin AOs) in CAS space'
)
dump_mat.dump_rec(log.stdout,
mocas_b,
label,
start=1,
**kwargs)
else:
log.info(
'Natural alpha-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout,
mocas_a,
label,
start=1,
**kwargs)
log.info(
'Natural beta-orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout,
mocas_b,
label,
start=1,
**kwargs)
tol = getattr(__config__, 'mcscf_addons_map2hf_tol', 0.4)
s = reduce(numpy.dot,
(mo_coeff[0].T, ovlp_ao, self._scf.mo_coeff[0]))
idx = numpy.argwhere(abs(s) > tol)
for i, j in idx:
log.info('alpha <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
s = reduce(numpy.dot,
(mo_coeff[1].T, ovlp_ao, self._scf.mo_coeff[1]))
idx = numpy.argwhere(abs(s) > tol)
for i, j in idx:
log.info('beta <mo-mcscf|mo-hf> %d %d %12.8f' %
(i + 1, j + 1, s[i, j]))
if hasattr(self.fcisolver, 'large_ci') and ci is not None:
log.info('\n** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, state in enumerate(ci):
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient',
i)
res = self.fcisolver.large_ci(state,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(
' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient'
)
res = self.fcisolver.large_ci(ci,
self.ncas,
self.nelecas,
large_ci_tol,
return_strs=False)
for c, ia, ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
return dm1a, dm1b
def cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
casdm1=None, verbose=None):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy. Be careful with this
option since the resultant natural orbitals might have the
different symmetry to the irreps indicated by CASSCF.orbsym
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mc.stdout, mc.verbose)
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
# orbital symmetry is reserved in this _eig call
occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
idx = numpy.argsort(occ)
occ = occ[idx]
ucas = ucas[:,idx]
# restore phase
# where_natorb gives the location of the natural orbital for the input cas
# orbitals. gen_strings4orblist map thes sorted strings (on CAS orbital) to
# the unsorted determinant strings (on natural orbital). e.g. (3o,2e) system
# CAS orbital 1 2 3
# natural orbital 3 1 2 <= by mo_1to1map
# CASorb-strings 0b011, 0b101, 0b110
# == (1,2), (1,3), (2,3)
# natorb-strings (3,1), (3,2), (1,2)
# == 0B101, 0B110, 0B011 <= by gen_strings4orblist
# then argsort to translate the string representation to the address
# [2(=0B011), 0(=0B101), 1(=0B110)]
# to indicate which CASorb-strings address to be loaded in each natorb-strings slot
where_natorb = mo_1to1map(ucas)
for i, k in enumerate(where_natorb):
if ucas[i,k] < 0:
ucas[:,k] *= -1
occ = -occ
mo_occ = numpy.zeros(mo_coeff.shape[1])
mo_occ[:ncore] = 2
mo_occ[ncore:nocc] = occ
if isinstance(ci, numpy.ndarray):
fcivec = fci.addons.transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
elif isinstance(ci, (tuple, list)) and isinstance(ci[0], numpy.ndarray):
# for state-average eigenfunctions
fcivec = [fci.addons.transform_ci_for_orbital_rotation(x, ncas, nelecas, ucas)
for x in ci]
else:
log.info('FCI vector not available, call CASCI for wavefunction')
mocas = mo_coeff1[:,ncore:nocc]
h1eff = reduce(numpy.dot, (mocas.T, mc.get_hcore(), mocas))
if eris is not None and hasattr(eris, 'ppaa'):
h1eff += reduce(numpy.dot, (ucas.T, eris.vhf_c[ncore:nocc,ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc,ncore:nocc,:,:], ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
dm_core = numpy.dot(mo_coeff[:,:ncore]*2, mo_coeff[:,:ncore].T)
vj, vk = mc._scf.get_jk(mc.mol, dm_core)
h1eff += reduce(numpy.dot, (mocas.T, vj-vk*.5, mocas))
aaaa = ao2mo.kernel(mc.mol, mocas)
max_memory = max(400, mc.max_memory-lib.current_memory()[0])
e_cas, fcivec = mc.fcisolver.kernel(h1eff, aaaa, ncas, nelecas,
max_memory=max_memory, verbose=log)
log.debug('In Natural orbital, CI energy = %.12g', e_cas)
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:,ncore:nocc] = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
if log.verbose >= logger.INFO:
ovlp_ao = mc._scf.get_ovlp()
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(occ))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.spheric_labels(True)
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff1[:,ncore:nocc]))
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:,ncore:nocc].T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s[i,j])
return mo_coeff1, fcivec, mo_occ
def analyze(self, verbose=None, **kwargs):
if verbose is None: verbose = self.verbose
from pyscf.lo import orth
from pyscf.tools import dump_mat
if not self.mol.symmetry:
return rohf.ROHF.analyze(self, verbose, **kwargs)
mo_energy = self.mo_energy
mo_occ = self.mo_occ
mo_coeff = self.mo_coeff
log = logger.Logger(self.stdout, verbose)
mol = self.mol
nirrep = len(mol.irrep_id)
ovlp_ao = self.get_ovlp()
orbsym = get_orbsym(self.mol, mo_coeff)
wfnsym = 0
ndoccs = []
nsoccs = []
for k,ir in enumerate(mol.irrep_id):
ndoccs.append(sum(orbsym[mo_occ==2] == ir))
nsoccs.append(sum(orbsym[mo_occ==1] == ir))
if nsoccs[k] % 2:
wfnsym ^= ir
if mol.groupname in ('Dooh', 'Coov'):
log.info('TODO: total symmetry for %s', mol.groupname)
else:
log.info('total symmetry = %s',
symm.irrep_id2name(mol.groupname, wfnsym))
log.info('occupancy for each irrep: ' + (' %4s'*nirrep),
*mol.irrep_name)
log.info('double occ ' + (' %4d'*nirrep), *ndoccs)
log.info('single occ ' + (' %4d'*nirrep), *nsoccs)
log.info('**** MO energy ****')
irname_full = {}
for k,ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
if self._focka_ao is None:
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%-3d (%s #%-2d), energy= %-18.15g occ= %g',
k+1, irname_full[j], irorbcnt[j],
mo_energy[k], mo_occ[k])
else:
mo_ea = numpy.einsum('ik,ik->k', mo_coeff, self._focka_ao.dot(mo_coeff))
mo_eb = numpy.einsum('ik,ik->k', mo_coeff, self._fockb_ao.dot(mo_coeff))
log.note(' Roothaan | alpha | beta')
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%-4d(%-3s #%-2d) energy= %-18.15g | %-18.15g | %-18.15g occ= %g',
k+1, irname_full[j], irorbcnt[j],
mo_energy[k], mo_ea[k], mo_eb[k], mo_occ[k])
if verbose >= logger.DEBUG:
label = mol.ao_labels()
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(self.stdout, c, label, molabel, start=1, **kwargs)
dm = self.make_rdm1(mo_coeff, mo_occ)
return self.mulliken_meta(mol, dm, s=ovlp_ao, verbose=verbose)
def __init__(self,
the_mf,
active_orbs,
localizationtype,
ao_rotation=None,
use_full_hessian=True,
localization_threshold=1e-6):
assert ((localizationtype == 'meta_lowdin')
or (localizationtype == 'boys')
or (localizationtype == 'lowdin')
or (localizationtype == 'iao'))
self.num_mf_stab_checks = 0
# Information on the full HF problem
self.mol = the_mf.mol
self._scf = the_mf
self.max_memory = the_mf.max_memory
self.get_jk_ao = partial(the_mf.get_jk, self.mol)
self.get_veff_ao = partial(the_mf.get_veff, self.mol)
self.get_k_ao = partial(the_mf.get_k, self.mol)
self.fullovlpao = the_mf.get_ovlp
self.fullEhf = the_mf.e_tot
self.fullRDM_ao = np.asarray(the_mf.make_rdm1())
if self.fullRDM_ao.ndim == 3:
self.fullSDM_ao = self.fullRDM_ao[0] - self.fullRDM_ao[1]
self.fullRDM_ao = self.fullRDM_ao[0] + self.fullRDM_ao[1]
else:
self.fullSDM_ao = np.zeros_like(self.fullRDM_ao)
self.fullJK_ao = self.get_veff_ao(
dm=self.fullRDM_ao, dm_last=0, vhf_last=0,
hermi=1) #Last 3 numbers: dm_last, vhf_last, hermi
if self.fullJK_ao.ndim == 3:
self.fullJK_ao = self.fullJK_ao[0]
# Because I gave it a spin-summed 1-RDM, the two spins for JK will necessarily be identical
self.fullFOCK_ao = the_mf.get_hcore() + self.fullJK_ao
self.e_tot = the_mf.e_tot
self.x2c = isinstance(the_mf, x2c._X2C_SCF)
# Active space information
self._which = localizationtype
self.active = np.zeros([self.mol.nao_nr()], dtype=int)
self.active[active_orbs] = 1
self.norbs_tot = np.sum(self.active) # Number of active space orbitals
self.nelec_tot = int(
np.rint(self.mol.nelectron -
np.sum(the_mf.mo_occ[self.active == 0]))
) # Total number of electrons minus frozen part
# Localize the orbitals
if ((self._which == 'meta_lowdin') or (self._which == 'boys')):
if (self._which == 'meta_lowdin'):
assert (self.norbs_tot == self.mol.nao_nr()
) # Full active space required
if (self._which == 'boys'):
self.ao2loc = the_mf.mo_coeff[:, self.active == 1]
if (self.norbs_tot == self.mol.nao_nr()
): # If you want the full active, do meta-Lowdin
nao.AOSHELL[4] = ['1s0p0d0f', '2s1p0d0f'
] # redefine the valence shell for Be
self.ao2loc = orth.orth_ao(self.mol, 'meta_lowdin')
if (ao_rotation != None):
self.ao2loc = np.dot(self.ao2loc, ao_rotation.T)
if (self._which == 'boys'):
old_verbose = self.mol.verbose
self.mol.verbose = 5
loc = boys.Boys(self.mol, self.ao2loc)
# loc = localizer.localizer( self.mol, self.ao2loc, self._which, use_full_hessian )
self.mol.verbose = old_verbose
# self.ao2loc = loc.optimize( threshold=localization_threshold )
self.ao2loc = loc.kernel()
self.TI_OK = False # Check yourself if OK, then overwrite
if (self._which == 'lowdin'):
assert (self.norbs_tot == self.mol.nao_nr()
) # Full active space required
ovlp = self.mol.intor('cint1e_ovlp_sph')
ovlp_eigs, ovlp_vecs = np.linalg.eigh(ovlp)
assert (np.linalg.norm(
np.dot(np.dot(ovlp_vecs, np.diag(ovlp_eigs)), ovlp_vecs.T) -
ovlp) < 1e-10)
self.ao2loc = np.dot(
np.dot(ovlp_vecs, np.diag(np.power(ovlp_eigs, -0.5))),
ovlp_vecs.T)
self.TI_OK = False # Check yourself if OK, then overwrite
if (self._which == 'iao'):
assert (self.norbs_tot == self.mol.nao_nr()
) # Full active space assumed
self.ao2loc = iao_helper.localize_iao(self.mol, the_mf)
if (ao_rotation != None):
self.ao2loc = np.dot(self.ao2loc, ao_rotation.T)
self.TI_OK = False # Check yourself if OK, then overwrite
#self.molden( 'dump.molden' ) # Debugging mode
assert (self.loc_ortho() < 1e-8)
# Stored inverse overlap matrix
self.ao_ovlp_inv = np.dot(self.ao2loc, self.ao2loc.conjugate().T)
self.ao_ovlp = the_mf.get_ovlp()
assert (is_matrix_eye(np.dot(self.ao_ovlp, self.ao_ovlp_inv)))
# Effective Hamiltonian due to frozen part
self.frozenDM_mo = np.array(the_mf.mo_occ, copy=True)
self.frozenDM_mo[self.active ==
1] = 0 # Only the frozen MO occupancies nonzero
self.frozenDM_ao = np.dot(
np.dot(the_mf.mo_coeff, np.diag(self.frozenDM_mo)),
the_mf.mo_coeff.T)
self.frozenJK_ao = self.get_veff_ao(
self.frozenDM_ao, 0, 0,
1) #Last 3 numbers: dm_last, vhf_last, hermi
if self.frozenJK_ao.ndim == 3:
self.frozenJK_ao = self.frozenJK_ao[0]
# Because I gave it a spin-summed 1-RDM, the two spins for JK will necessarily be identical
self.frozenOEI_ao = self.fullFOCK_ao - self.fullJK_ao + self.frozenJK_ao
# Localized OEI and ERI
self.activeCONST = self.mol.energy_nuc() + np.einsum(
'ij,ij->', self.frozenOEI_ao - 0.5 * self.frozenJK_ao,
self.frozenDM_ao)
self.activeOEI = represent_operator_in_basis(self.frozenOEI_ao,
self.ao2loc)
self.activeFOCK = represent_operator_in_basis(self.fullFOCK_ao,
self.ao2loc)
self.activeVSPIN = np.zeros_like(
self.activeFOCK) # FIXME: correct behavior for ROHF init!
self.activeJKidem = self.activeFOCK - self.activeOEI
self.activeJKcorr = np.zeros((self.norbs_tot, self.norbs_tot),
dtype=self.activeOEI.dtype)
self.oneRDM_loc = self.ao2loc.conjugate(
).T @ self.ao_ovlp @ self.fullRDM_ao @ self.ao_ovlp @ self.ao2loc
self.oneSDM_loc = self.ao2loc.conjugate(
).T @ self.ao_ovlp @ self.fullSDM_ao @ self.ao_ovlp @ self.ao2loc
self.oneRDMcorr_loc = np.zeros((self.norbs_tot, self.norbs_tot),
dtype=self.activeOEI.dtype)
self.loc2idem = np.eye(self.norbs_tot, dtype=self.activeOEI.dtype)
self.nelec_idem = self.nelec_tot
self._eri = None
self.with_df = None
assert (abs(np.trace(self.oneRDM_loc) - self.nelec_tot) <
1e-8), '{} {}'.format(np.trace(self.oneRDM_loc),
self.nelec_tot)
sys.stdout.flush()
def _is_mem_enough():
return 2 * (self.norbs_tot**
4) / 1e6 + current_memory()[0] < self.max_memory * 0.95
# Unfortunately, there is currently no way to do the integral transformation directly on the antisymmetrized two-electron
# integrals, at least none already implemented in PySCF. Therefore the smallest possible memory footprint involves
# two arrays of fourfold symmetry, which works out to roughly one half of an array with no symmetry
if hasattr(the_mf, 'with_df') and hasattr(
the_mf.with_df,
'_cderi') and the_mf.with_df._cderi is not None:
print("Found density-fitting three-center integrals scf object")
loc2ao = self.ao2loc.conjugate().T
locOao = np.dot(loc2ao, self.ao_ovlp)
self.with_df = the_mf.with_df
self.with_df.loc2eri_bas = lambda x: np.dot(self.ao2loc, x)
self.with_df.loc2eri_op = lambda x: reduce(np.dot, (self.ao2loc, x,
loc2ao))
self.with_df.eri2loc_bas = lambda x: np.dot(locOao, x)
self.with_df.eri2loc_op = lambda x: reduce(np.dot, (loc2ao, x, self
.ao2loc))
elif the_mf._eri is not None:
print("Found eris on scf object")
loc2ao = self.ao2loc.conjugate().T
locOao = np.dot(loc2ao, self.ao_ovlp)
self._eri = the_mf._eri
self._eri = tag_array(self._eri,
loc2eri_bas=lambda x: np.dot(self.ao2loc, x))
self._eri = tag_array(
self._eri,
loc2eri_op=lambda x: reduce(np.dot, (self.ao2loc, x, loc2ao)))
self._eri = tag_array(self._eri,
eri2loc_bas=lambda x: np.dot(locOao, x))
self._eri = tag_array(
self._eri,
eri2loc_op=lambda x: reduce(np.dot, (loc2ao, x, self.ao2loc)))
elif _is_mem_enough():
print("Storing eris in memory")
self._eri = ao2mo.restore(
8,
ao2mo.outcore.full_iofree(self.mol, self.ao2loc, compact=True),
self.norbs_tot)
self._eri = tag_array(self._eri, loc2eri_bas=lambda x: x)
self._eri = tag_array(self._eri, loc2eri_op=lambda x: x)
self._eri = tag_array(self._eri, eri2loc_bas=lambda x: x)
self._eri = tag_array(self._eri, eri2loc_op=lambda x: x)
else:
print("Direct calculation")
sys.stdout.flush()
# Symmetry information
try:
self.loc2symm = [
orthonormalize_a_basis(scipy.linalg.solve(self.ao2loc, ao2ir))
for ao2ir in self.mol.symm_orb
]
self.symmetry = self.mol.groupname
self.wfnsym = the_mf.wfnsym
self.ir_names = self.mol.irrep_name
self.ir_ids = self.mol.irrep_id
self.enforce_symmetry = True
except (AttributeError, TypeError) as e:
if self.mol.symmetry: raise (e)
self.loc2symm = [np.eye(self.norbs_tot)]
self.symmetry = False
self.wfnsym = 'A'
self.ir_names = ['A']
self.ir_ids = [0]
self.enforce_symmetry = False
print("Initial loc2symm nonorthonormality: {}".format(
measure_basis_nonorthonormality(
np.concatenate(self.loc2symm, axis=1))))
for loc2ir1, loc2ir2 in itertools.combinations(self.loc2symm, 2):
proj = loc2ir1 @ loc2ir1.conjugate().T
loc2ir2[:, :] -= proj @ loc2ir2
for loc2ir in self.loc2symm:
loc2ir[:, :] = orthonormalize_a_basis(loc2ir)
print("Final loc2symm nonorthonormality: {}".format(
measure_basis_nonorthonormality(
np.concatenate(self.loc2symm, axis=1))))
def analyze(mf, verbose=logger.DEBUG, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
mol = mf.mol
if not mol.symmetry:
return uhf.analyze(mf, verbose, with_meta_lowdin, **kwargs)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
ovlp_ao = mf.get_ovlp()
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsyma, orbsymb = get_orbsym(mf.mol, mo_coeff, ovlp_ao, False)
tot_sym = 0
noccsa = [sum(orbsyma[mo_occ[0]>0]==ir) for ir in mol.irrep_id]
noccsb = [sum(orbsymb[mo_occ[1]>0]==ir) for ir in mol.irrep_id]
for i, ir in enumerate(mol.irrep_id):
if (noccsa[i]+noccsb[i]) % 2:
tot_sym ^= ir
if mol.groupname in ('Dooh', 'Coov', 'SO3'):
log.note('TODO: total wave-function symmetry for %s', mol.groupname)
else:
log.note('Wave-function symmetry = %s',
symm.irrep_id2name(mol.groupname, tot_sym))
log.note('alpha occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsa)
log.note('beta occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsb)
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('alpha MO #%d (%s #%d), energy= %.15g occ= %g',
k+MO_BASE, irname_full[j], irorbcnt[j],
mo_energy[0][k], mo_occ[0][k])
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('beta MO #%d (%s #%d), energy= %.15g occ= %g',
k+MO_BASE, irname_full[j], irorbcnt[j],
mo_energy[1][k], mo_occ[1][k])
if mf.verbose >= logger.DEBUG:
label = mol.ao_labels()
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k+MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(' ** alpha MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
mo = c_inv.dot(mo_coeff[0])
else:
log.debug(' ** alpha MO coefficients (expansion on AOs) **')
mo = mo_coeff[0]
dump_mat.dump_rec(mf.stdout, mo, label, start=MO_BASE, **kwargs)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k+MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(' ** beta MO coefficients (expansion on meta-Lowdin AOs) **')
mo = c_inv.dot(mo_coeff[1])
else:
log.debug(' ** beta MO coefficients (expansion on AOs) **')
mo = mo_coeff[1]
dump_mat.dump_rec(mol.stdout, mo, label, molabel, start=MO_BASE, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
pop_and_charge = mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
else:
pop_and_charge = mf.mulliken_pop(mol, dm, s=ovlp_ao, verbose=log)
dip = mf.dip_moment(mol, dm, verbose=log)
return pop_and_charge, dip
def analyze(self, verbose=logger.DEBUG):
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = self.mo_energy
mo_occ = self.mo_occ
mo_coeff = self.mo_coeff
log = logger.Logger(self.stdout, verbose)
mol = self.mol
nirrep = len(mol.irrep_id)
ovlp_ao = self.get_ovlp()
orbsym = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mo_coeff,
s=ovlp_ao)
orbsym = numpy.array(orbsym)
wfnsym = 0
ndoccs = []
nsoccs = []
for k,ir in enumerate(mol.irrep_id):
ndoccs.append(sum(orbsym[mo_occ==2] == ir))
nsoccs.append(sum(orbsym[mo_occ==1] == ir))
if nsoccs[k] % 2:
wfnsym ^= ir
if mol.groupname in ('Dooh', 'Coov'):
log.info('TODO: total symmetry for %s', mol.groupname)
else:
log.info('total symmetry = %s',
symm.irrep_id2name(mol.groupname, wfnsym))
log.info('occupancy for each irrep: ' + (' %4s'*nirrep),
*mol.irrep_name)
log.info('double occ ' + (' %4d'*nirrep), *ndoccs)
log.info('single occ ' + (' %4d'*nirrep), *nsoccs)
log.info('**** MO energy ****')
irname_full = {}
for k,ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
if self._focka_ao is None:
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%-3d (%s #%-2d), energy= %-18.15g occ= %g',
k+1, irname_full[j], irorbcnt[j],
mo_energy[k], mo_occ[k])
else:
mo_ea = numpy.einsum('ik,ik->k', mo_coeff, self._focka_ao.dot(mo_coeff))
mo_eb = numpy.einsum('ik,ik->k', mo_coeff, self._fockb_ao.dot(mo_coeff))
log.note(' Roothaan | alpha | beta')
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%-4d(%-3s #%-2d) energy= %-18.15g | %-18.15g | %-18.15g occ= %g',
k+1, irname_full[j], irorbcnt[j],
mo_energy[k], mo_ea[k], mo_eb[k], mo_occ[k])
if verbose >= logger.DEBUG:
label = mol.spheric_labels(True)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(self.stdout, c, label, molabel, start=1)
dm = self.make_rdm1(mo_coeff, mo_occ)
return self.mulliken_meta(mol, dm, s=ovlp_ao, verbose=verbose)
def cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
casdm1=None, verbose=None):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy. Be careful with this
option since the resultant natural orbitals might have the
different symmetry to the irreps indicated by CASSCF.orbsym
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mc.stdout, mc.verbose)
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
idx = numpy.argsort(occ)
occ = occ[idx]
ucas = ucas[:,idx]
occ = -occ
# where_natorb gives the location of the natural orbital for the input cas
# orbitals. gen_strings4orblist map thes sorted strings (on CAS orbital) to
# the unsorted determinant strings (on natural orbital). e.g. (3o,2e) system
# CAS orbital 1 2 3
# natural orbital 3 1 2 <= by mo_1to1map
# CASorb-strings 0b011, 0b101, 0b110
# == (1,2), (1,3), (2,3)
# natorb-strings (3,1), (3,2), (1,2)
# == 0B101, 0B110, 0B011 <= by gen_strings4orblist
# then argsort to translate the string representation to the address
# [2(=0B011), 0(=0B101), 1(=0B110)]
# to indicate which CASorb-strings address to be loaded in each natorb-strings slot
where_natorb = mo_1to1map(ucas)
#guide_stringsa = fci.cistring.gen_strings4orblist(where_natorb, nelecas[0])
#guide_stringsb = fci.cistring.gen_strings4orblist(where_natorb, nelecas[1])
#old_det_idxa = numpy.argsort(guide_stringsa)
#old_det_idxb = numpy.argsort(guide_stringsb)
#ci0 = ci[old_det_idxa[:,None],old_det_idxb]
if isinstance(ci, numpy.ndarray):
ci0 = fci.addons.reorder(ci, nelecas, where_natorb)
elif isinstance(ci, (tuple, list)) and isinstance(ci[0], numpy.ndarray):
# for state-average eigenfunctions
ci0 = [fci.addons.reorder(x, nelecas, where_natorb) for x in ci]
else:
log.info('FCI vector not available, so not using old wavefunction as initial guess')
ci0 = None
# restore phase, to ensure the reordered ci vector is the correct initial guess
for i, k in enumerate(where_natorb):
if ucas[i,k] < 0:
ucas[:,k] *= -1
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:,ncore:nocc] = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
if log.verbose >= logger.INFO:
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(occ))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.spheric_labels(True)
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff1[:,ncore:nocc]))
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:,ncore:nocc].T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s[i,j])
mocas = mo_coeff1[:,ncore:nocc]
h1eff = reduce(numpy.dot, (mocas.T, mc.get_hcore(), mocas))
if eris is not None and hasattr(eris, 'ppaa'):
h1eff += reduce(numpy.dot, (ucas.T, eris.vhf_c[ncore:nocc,ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc,ncore:nocc,:,:], ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
dm_core = numpy.dot(mo_coeff[:,:ncore]*2, mo_coeff[:,:ncore].T)
vj, vk = mc._scf.get_jk(mc.mol, dm_core)
h1eff += reduce(numpy.dot, (mocas.T, vj-vk*.5, mocas))
aaaa = ao2mo.kernel(mc.mol, mocas)
e_cas, fcivec = mc.fcisolver.kernel(h1eff, aaaa, ncas, nelecas, ci0=ci0)
log.debug('In Natural orbital, CI energy = %.12g', e_cas)
return mo_coeff1, fcivec, occ
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.spheric_labels(True)
if hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff[:,ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i+1, j+1, s[i,j])
if ci is not None and numpy.ndim(ci) >= 2:
log.info('** Largest CI components **')
if ci[0].ndim == 2:
for i, state in enumerate(ci):
log.info(' string alpha, string beta, state %d CI coefficients', i)
for c,ia,ib in fci.addons.large_ci(state, casscf.ncas, casscf.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficients')
for c,ia,ib in fci.addons.large_ci(ci, casscf.ncas, casscf.nelecas):
log.info(' %9s %9s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(mf,
verbose=logger.DEBUG,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Occupancy for each irreps; Mulliken population analysis
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mol = mf.mol
if not mol.symmetry:
return hf.analyze(mf, verbose, with_meta_lowdin, **kwargs)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
ovlp_ao = mf.get_ovlp()
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
nirrep = len(mol.irrep_id)
orbsym = get_orbsym(mf.mol, mo_coeff, ovlp_ao, False)
wfnsym = 0
noccs = [sum(orbsym[mo_occ > 0] == ir) for ir in mol.irrep_id]
if mol.groupname in ('SO3', 'Dooh', 'Coov'):
log.note('TODO: total wave-function symmetry for %s',
mol.groupname)
else:
log.note('Wave-function symmetry = %s',
symm.irrep_id2name(mol.groupname, wfnsym))
log.note('occupancy for each irrep: ' + (' %4s' * nirrep),
*mol.irrep_name)
log.note(' ' + (' %4d' * nirrep), *noccs)
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%d (%s #%d), energy= %.15g occ= %g', k + MO_BASE,
irname_full[j], irorbcnt[j], mo_energy[k], mo_occ[k])
if log.verbose >= logger.DEBUG:
label = mol.ao_labels()
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k + MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
else:
log.debug(' ** MO coefficients (expansion on AOs) **')
c = mo_coeff
dump_mat.dump_rec(mf.stdout,
c,
label,
molabel,
start=MO_BASE,
**kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
pop_and_charge = mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
else:
pop_and_charge = mf.mulliken_pop(mol, dm, s=ovlp_ao, verbose=log)
dip = mf.dip_moment(mol, dm, verbose=log)
return pop_and_charge, dip
def analyze(casscf, mo_coeff=None, ci=None, verbose=None,
large_ci_tol=LARGE_CI_TOL, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
log = logger.new_logger(casscf, verbose)
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
label = casscf.mol.ao_labels()
if (isinstance(ci, (list, tuple)) and
not isinstance(casscf.fcisolver, addons.StateAverageFCISolver)):
log.warn('Mulitple states found in CASCI/CASSCF solver. Density '
'matrix of first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
if getattr(casscf.fcisolver, 'make_rdm1s', None):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(civec, ncas, nelecas)
casdm1 = casdm1a + casdm1b
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG2:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(civec, ncas, nelecas)
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
mocas = numpy.dot(mocas, ucas)
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mocas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas, label, start=1, **kwargs)
if log.verbose >= logger.DEBUG2:
if not casscf.natorb:
log.debug2('NOTE: mc.mo_coeff in active space is different to '
'the natural orbital coefficients printed in above.')
if with_meta_lowdin:
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
log.debug2('MCSCF orbital (expansion on meta-Lowdin AOs)')
else:
c = mo_coeff
log.debug2('MCSCF orbital (expansion on AOs)')
dump_mat.dump_rec(log.stdout, c, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
addons.map2hf(casscf, casscf._scf.mo_coeff)
if getattr(casscf.fcisolver, 'large_ci', None) and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
if with_meta_lowdin:
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
else:
casscf._scf.mulliken_pop(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(casscf, mo_coeff=None, ci=None, verbose=None,
large_ci_tol=LARGE_CI_TOL, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
log = logger.new_logger(casscf, verbose)
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
label = casscf.mol.ao_labels()
if (isinstance(ci, (list, tuple, RANGE_TYPE)) and
not isinstance(casscf.fcisolver, addons.StateAverageFCISolver)):
log.warn('Mulitple states found in CASCI/CASSCF solver. Density '
'matrix of the first state is generated in .analyze() function.')
civec = ci[0]
else:
civec = ci
if getattr(casscf.fcisolver, 'make_rdm1s', None):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(civec, ncas, nelecas)
casdm1 = casdm1a + casdm1b
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG2:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(civec, ncas, nelecas)
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
mocas = numpy.dot(mocas, ucas)
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mocas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mocas))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mocas, label, start=1, **kwargs)
if log.verbose >= logger.DEBUG2:
if not casscf.natorb:
log.debug2('NOTE: mc.mo_coeff in active space is different to '
'the natural orbital coefficients printed in above.')
if with_meta_lowdin:
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
log.debug2('MCSCF orbital (expansion on meta-Lowdin AOs)')
else:
c = mo_coeff
log.debug2('MCSCF orbital (expansion on AOs)')
dump_mat.dump_rec(log.stdout, c, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
addons.map2hf(casscf, casscf._scf.mo_coeff)
if (ci is not None and
(getattr(casscf.fcisolver, 'large_ci', None) or
getattr(casscf.fcisolver, 'states_large_ci', None))):
log.info('** Largest CI components **')
if isinstance(ci, (list, tuple, RANGE_TYPE)):
if hasattr(casscf.fcisolver, 'states_large_ci'):
# defined in state_average_mix_ mcscf object
res = casscf.fcisolver.states_large_ci(ci, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
else:
res = [casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
for civec in ci]
for i, civec in enumerate(ci):
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
for c,ia,ib in res[i]:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
if with_meta_lowdin:
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
else:
casscf._scf.mulliken_pop(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
casdm1=None, verbose=None, with_meta_lowdin=WITH_META_LOWDIN):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
accordingly
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy.
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
log = logger.new_logger(mc, verbose)
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
nmo = mo_coeff.shape[1]
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
# orbital symmetry is reserved in this _eig call
cas_occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
casorb_idx = numpy.argsort(cas_occ.round(9), kind='mergesort')
cas_occ = cas_occ[casorb_idx]
ucas = ucas[:,casorb_idx]
cas_occ = -cas_occ
mo_occ = numpy.zeros(mo_coeff.shape[1])
mo_occ[:ncore] = 2
mo_occ[ncore:nocc] = cas_occ
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:,ncore:nocc] = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
if getattr(mo_coeff, 'orbsym', None) is not None:
orbsym = numpy.copy(mo_coeff.orbsym)
if sort:
orbsym[ncore:nocc] = orbsym[ncore:nocc][casorb_idx]
mo_coeff1 = lib.tag_array(mo_coeff1, orbsym=orbsym)
else:
orbsym = numpy.zeros(nmo, dtype=int)
# When occupancies of active orbitals equal to 2 or 0, these orbitals
# need to be canonicalized along with inactive(core or virtual) orbitals
# using general Fock matrix. Because they are strongly coupled with
# inactive orbitals, the 0th order Hamiltonian of MRPT methods can be
# strongly affected. Numerical uncertainty may be found in the perturbed
# correlation energy.
# See issue https://github.com/pyscf/pyscf/issues/1041
occ2_idx = numpy.where(2 - cas_occ < FRAC_OCC_THRESHOLD)[0]
occ0_idx = numpy.where(cas_occ < FRAC_OCC_THRESHOLD)[0]
if occ2_idx.size > 0 or occ0_idx.size > 0:
fock_ao = mc.get_fock(mo_coeff, ci, eris, casdm1, verbose)
def _diag_subfock_(idx):
c = mo_coeff1[:,idx]
fock = reduce(numpy.dot, (c.conj().T, fock_ao, c))
w, c = mc._eig(fock, None, None, orbsym[idx])
mo_coeff1[:,idx] = mo_coeff1[:,idx].dot(c)
if occ2_idx.size > 0:
log.warn('Active orbitals %s (occs = %s) are canonicalized with core orbitals',
occ2_idx, cas_occ[occ2_idx])
full_occ2_idx = numpy.append(numpy.arange(ncore), ncore + occ2_idx)
_diag_subfock_(full_occ2_idx)
if occ0_idx.size > 0:
log.warn('Active orbitals %s (occs = %s) are canonicalized with external orbitals',
occ0_idx, cas_occ[occ0_idx])
full_occ0_idx = numpy.append(ncore + occ0_idx, numpy.arange(nocc, nmo))
_diag_subfock_(full_occ0_idx)
# Rotate CI according to the unitary coefficients ucas if applicable
fcivec = None
if getattr(mc.fcisolver, 'transform_ci_for_orbital_rotation', None):
if isinstance(ci, numpy.ndarray):
fcivec = mc.fcisolver.transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
elif (isinstance(ci, (list, tuple)) and
all(isinstance(x[0], numpy.ndarray) for x in ci)):
fcivec = [mc.fcisolver.transform_ci_for_orbital_rotation(x, ncas, nelecas, ucas)
for x in ci]
elif getattr(mc.fcisolver, 'states_transform_ci_for_orbital_rotation', None):
fcivec = mc.fcisolver.states_transform_ci_for_orbital_rotation(ci, ncas, nelecas, ucas)
# Rerun fcisolver to get wavefunction if it cannot be transformed from
# existed one.
if fcivec is None:
log.info('FCI vector not available, call CASCI to update wavefunction')
mocas = mo_coeff1[:,ncore:nocc]
hcore = mc.get_hcore()
dm_core = numpy.dot(mo_coeff1[:,:ncore]*2, mo_coeff1[:,:ncore].conj().T)
ecore = mc.energy_nuc()
ecore+= numpy.einsum('ij,ji', hcore, dm_core)
h1eff = reduce(numpy.dot, (mocas.conj().T, hcore, mocas))
if getattr(eris, 'ppaa', None) is not None:
ecore += eris.vhf_c[:ncore,:ncore].trace()
h1eff += reduce(numpy.dot, (ucas.conj().T, eris.vhf_c[ncore:nocc,ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc,ncore:nocc,:,:], ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
if getattr(mc, 'with_df', None):
aaaa = mc.with_df.ao2mo(mocas)
else:
aaaa = ao2mo.kernel(mc.mol, mocas)
corevhf = mc.get_veff(mc.mol, dm_core)
ecore += numpy.einsum('ij,ji', dm_core, corevhf) * .5
h1eff += reduce(numpy.dot, (mocas.conj().T, corevhf, mocas))
# See label_symmetry_ function in casci_symm.py which initialize the
# orbital symmetry information in fcisolver. This orbital symmetry
# labels should be reordered to match the sorted active space orbitals.
if sort and getattr(mo_coeff1, 'orbsym', None) is not None:
mc.fcisolver.orbsym = mo_coeff1.orbsym[ncore:nocc]
max_memory = max(400, mc.max_memory-lib.current_memory()[0])
e, fcivec = mc.fcisolver.kernel(h1eff, aaaa, ncas, nelecas, ecore=ecore,
max_memory=max_memory, verbose=log)
log.debug('In Natural orbital, CASCI energy = %s', e)
if log.verbose >= logger.INFO:
ovlp_ao = mc._scf.get_ovlp()
# where_natorb gives the new locations of the natural orbitals
where_natorb = mo_1to1map(ucas)
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(cas_occ))
if with_meta_lowdin:
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.ao_labels()
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.conj().T, ovlp_ao, mo_coeff1[:,ncore:nocc]))
else:
log.info('Natural orbital (expansion on AOs) in CAS space')
label = mc.mol.ao_labels()
mo_cas = mo_coeff1[:,ncore:nocc]
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:,ncore:nocc].conj().T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f',
ncore+i+1, j+1, s[i,j])
return mo_coeff1, fcivec, mo_occ
def cas_natorb(mc,
mo_coeff=None,
ci=None,
eris=None,
sort=False,
casdm1=None,
verbose=None):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
Args:
mc : a CASSCF/CASCI object or RHF object
Kwargs:
sort : bool
Sort natural orbitals wrt the occupancy.
Returns:
A tuple, the first item is natural orbitals, the second is updated CI
coefficients, the third is the natural occupancy associated to the
natural orbitals.
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
from pyscf.tools.mo_mapping import mo_1to1map
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mc.stdout, mc.verbose)
if mo_coeff is None: mo_coeff = mc.mo_coeff
if ci is None: ci = mc.ci
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
if casdm1 is None:
casdm1 = mc.fcisolver.make_rdm1(ci, ncas, nelecas)
# orbital symmetry is reserved in this _eig call
occ, ucas = mc._eig(-casdm1, ncore, nocc)
if sort:
casorb_idx = numpy.argsort(occ)
occ = occ[casorb_idx]
ucas = ucas[:, casorb_idx]
# restore phase
# where_natorb gives the location of the natural orbital for the input cas
# orbitals. gen_strings4orblist map thes sorted strings (on CAS orbital) to
# the unsorted determinant strings (on natural orbital). e.g. (3o,2e) system
# CAS orbital 1 2 3
# natural orbital 3 1 2 <= by mo_1to1map
# CASorb-strings 0b011, 0b101, 0b110
# == (1,2), (1,3), (2,3)
# natorb-strings (3,1), (3,2), (1,2)
# == 0B101, 0B110, 0B011 <= by gen_strings4orblist
# then argsort to translate the string representation to the address
# [2(=0B011), 0(=0B101), 1(=0B110)]
# to indicate which CASorb-strings address to be loaded in each natorb-strings slot
where_natorb = mo_1to1map(ucas)
for i, k in enumerate(where_natorb):
if ucas[i, k] < 0:
ucas[:, k] *= -1
occ = -occ
mo_occ = numpy.zeros(mo_coeff.shape[1])
mo_occ[:ncore] = 2
mo_occ[ncore:nocc] = occ
if isinstance(ci, numpy.ndarray):
fcivec = fci.addons.transform_ci_for_orbital_rotation(
ci, ncas, nelecas, ucas)
elif isinstance(ci, (tuple, list)) and isinstance(ci[0], numpy.ndarray):
# for state-average eigenfunctions
fcivec = [
fci.addons.transform_ci_for_orbital_rotation(
x, ncas, nelecas, ucas) for x in ci
]
else:
log.info('FCI vector not available, call CASCI for wavefunction')
mocas = mo_coeff[:, ncore:nocc]
h1eff = reduce(numpy.dot, (mocas.T, mc.get_hcore(), mocas))
if eris is not None and hasattr(eris, 'ppaa'):
h1eff += reduce(numpy.dot,
(ucas.T, eris.vhf_c[ncore:nocc, ncore:nocc], ucas))
aaaa = ao2mo.restore(4, eris.ppaa[ncore:nocc, ncore:nocc, :, :],
ncas)
aaaa = ao2mo.incore.full(aaaa, ucas)
else:
dm_core = numpy.dot(mo_coeff[:, :ncore] * 2, mo_coeff[:, :ncore].T)
vj, vk = mc._scf.get_jk(mc.mol, dm_core)
h1eff += reduce(numpy.dot, (mocas.T, vj - vk * .5, mocas))
aaaa = ao2mo.kernel(mc.mol, mocas)
max_memory = max(400, mc.max_memory - lib.current_memory()[0])
e_cas, fcivec = mc.fcisolver.kernel(h1eff,
aaaa,
ncas,
nelecas,
max_memory=max_memory,
verbose=log)
log.debug('In Natural orbital, CI energy = %.12g', e_cas)
mo_coeff1 = mo_coeff.copy()
mo_coeff1[:, ncore:nocc] = numpy.dot(mo_coeff[:, ncore:nocc], ucas)
if hasattr(mo_coeff, 'orbsym'):
orbsym = numpy.copy(mo_coeff.orbsym)
if sort:
orbsym[ncore:nocc] = orbsym[ncore:nocc][casorb_idx]
mo_coeff1 = lib.tag_array(mo_coeff1, orbsym=orbsym)
if log.verbose >= logger.INFO:
ovlp_ao = mc._scf.get_ovlp()
log.debug('where_natorb %s', str(where_natorb))
log.info('Natural occ %s', str(occ))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
label = mc.mol.ao_labels()
orth_coeff = orth.orth_ao(mc.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot,
(orth_coeff.T, ovlp_ao, mo_coeff1[:, ncore:nocc]))
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
if mc._scf.mo_coeff is not None:
s = reduce(numpy.dot, (mo_coeff1[:, ncore:nocc].T,
mc._scf.get_ovlp(), mc._scf.mo_coeff))
idx = numpy.argwhere(abs(s) > .4)
for i, j in idx:
log.info('<CAS-nat-orb|mo-hf> %d %d %12.8f', ncore + i + 1,
j + 1, s[i, j])
return mo_coeff1, fcivec, mo_occ
def analyze(mf, verbose=logger.DEBUG, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
mol = mf.mol
if not mol.symmetry:
return uhf.analyze(mf, verbose, with_meta_lowdin, **kwargs)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
ovlp_ao = mf.get_ovlp()
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsyma, orbsymb = get_orbsym(mf.mol, mo_coeff, ovlp_ao, False)
tot_sym = 0
noccsa = [sum(orbsyma[mo_occ[0]>0]==ir) for ir in mol.irrep_id]
noccsb = [sum(orbsymb[mo_occ[1]>0]==ir) for ir in mol.irrep_id]
for i, ir in enumerate(mol.irrep_id):
if (noccsa[i]+noccsb[i]) % 2:
tot_sym ^= ir
if mol.groupname in ('Dooh', 'Coov', 'SO3'):
log.note('TODO: total wave-function symmetry for %s', mol.groupname)
else:
log.note('Wave-function symmetry = %s',
symm.irrep_id2name(mol.groupname, tot_sym))
log.note('alpha occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsa)
log.note('beta occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsb)
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('alpha MO #%d (%s #%d), energy= %.15g occ= %g',
k+MO_BASE, irname_full[j], irorbcnt[j],
mo_energy[0][k], mo_occ[0][k])
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('beta MO #%d (%s #%d), energy= %.15g occ= %g',
k+MO_BASE, irname_full[j], irorbcnt[j],
mo_energy[1][k], mo_occ[1][k])
if mf.verbose >= logger.DEBUG:
label = mol.ao_labels()
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k+MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(' ** alpha MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.conj().T, ovlp_ao)
mo = c_inv.dot(mo_coeff[0])
else:
log.debug(' ** alpha MO coefficients (expansion on AOs) **')
mo = mo_coeff[0]
dump_mat.dump_rec(mf.stdout, mo, label, start=MO_BASE, **kwargs)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k+MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(' ** beta MO coefficients (expansion on meta-Lowdin AOs) **')
mo = c_inv.dot(mo_coeff[1])
else:
log.debug(' ** beta MO coefficients (expansion on AOs) **')
mo = mo_coeff[1]
dump_mat.dump_rec(mol.stdout, mo, label, molabel, start=MO_BASE, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
pop_and_charge = mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
else:
pop_and_charge = mf.mulliken_pop(mol, dm, s=ovlp_ao, verbose=log)
dip = mf.dip_moment(mol, dm, verbose=log)
return pop_and_charge, dip
def analyze(mf, verbose=logger.DEBUG):
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
mol = mf.mol
log = pyscf.lib.logger.Logger(mf.stdout, verbose)
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsyma = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff[0], s=ovlp_ao)
orbsymb = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff[1], s=ovlp_ao)
orbsyma = numpy.array(orbsyma)
orbsymb = numpy.array(orbsymb)
tot_sym = 0
noccsa = [sum(orbsyma[mo_occ[0]>0]==ir) for ir in mol.irrep_id]
noccsb = [sum(orbsymb[mo_occ[1]>0]==ir) for ir in mol.irrep_id]
for i, ir in enumerate(mol.irrep_id):
if (noccsa[i]+noccsb[i]) % 2:
tot_sym ^= ir
if mol.groupname in ('Dooh', 'Coov', 'SO3'):
log.note('TODO: total symmetry for %s', mol.groupname)
else:
log.note('total symmetry = %s',
symm.irrep_id2name(mol.groupname, tot_sym))
log.note('alpha occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsa)
log.note('beta occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsb)
ss, s = mf.spin_square((mo_coeff[0][:,mo_occ[0]>0],
mo_coeff[1][:,mo_occ[1]>0]), ovlp_ao)
log.note('multiplicity <S^2> = %.8g 2S+1 = %.8g', ss, s)
if verbose >= logger.NOTE:
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('alpha MO #%d (%s #%d), energy= %.15g occ= %g',
k+1, irname_full[j], irorbcnt[j], mo_energy[0][k], mo_occ[0][k])
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('beta MO #%d (%s #%d), energy= %.15g occ= %g',
k+1, irname_full[j], irorbcnt[j], mo_energy[1][k], mo_occ[1][k])
ovlp_ao = mf.get_ovlp()
if mf.verbose >= logger.DEBUG:
label = mol.spheric_labels(True)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** alpha MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
dump_mat.dump_rec(mol.stdout, c_inv.dot(mo_coeff[0]), label, molabel, start=1)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** beta MO coefficients (expansion on meta-Lowdin AOs) **')
dump_mat.dump_rec(mol.stdout, c_inv.dot(mo_coeff[1]), label, molabel, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
def __init__(self,
the_mf,
active_orbs,
localizationtype,
ao_rotation=None,
use_full_hessian=True,
localization_threshold=1e-6):
assert ((localizationtype == 'meta_lowdin')
or (localizationtype == 'boys')
or (localizationtype == 'lowdin')
or (localizationtype == 'iao'))
# Information on the full SCF problem
self.mo_occ = the_mf.mo_occ
self.mol = the_mf.mol
self.s1e_ao = the_mf.get_ovlp()
self.fullEhf = the_mf.e_tot
#self.fullDMao = np.dot(np.dot( the_mf.mo_coeff, np.diag( the_mf.mo_occ )), the_mf.mo_coeff.T )
self.fullDMao = the_mf.make_rdm1()
#self.fullJKao = scf.hf.get_veff( self.mol, self.fullDMao, 0, 0, 1 ) #Last 3 numbers: dm_last, vhf_last, hermi
#self.fullJKao = the_mf.get_veff()
#self.fullFOCKao = self.mol.intor_symmetric('int1e_kin') + self.mol.intor_symmetric('int1e_nuc') + self.fullJKao
self.fullFOCKao = the_mf.get_fock()
self.fullOEIao = the_mf.get_hcore()
# Active space information
self._which = localizationtype
self.active = np.zeros([self.mol.nao_nr()], dtype=int)
self.active[active_orbs] = 1
self.NOrb = np.sum(self.active) # Number of active space orbitals
self.Nelec = int(
np.rint(self.mol.nelectron -
np.sum(the_mf.mo_occ[self.active == 0]))
) # Total number of electrons minus frozen part
# Localize the orbitals
if ((self._which == 'meta_lowdin') or (self._which == 'boys')):
if (self._which == 'meta_lowdin'):
assert (self.NOrb == self.mol.nao_nr()
) # Full active space required
if (self._which == 'boys'):
self.ao2loc = the_mf.mo_coeff[:, self.active == 1]
if (self.NOrb == self.mol.nao_nr()
): # If you want the full active, do meta-Lowdin
nao.AOSHELL[4] = ['1s0p0d0f', '2s1p0d0f'
] # redefine the valence shell for Be
self.ao2loc = orth.orth_ao(self.mol, 'meta_lowdin')
if (ao_rotation is not None):
self.ao2loc = np.dot(self.ao2loc, ao_rotation.T)
if (self._which == 'boys'):
old_verbose = self.mol.verbose
self.mol.verbose = 5
#loc = localizer.localizer( self.mol, self.ao2loc, self._which, use_full_hessian )
boys = Boys(self.mol, self.ao2loc)
self.mol.verbose = old_verbose
#self.ao2loc = loc.optimize( threshold=localization_threshold )
self.ao2loc = boys.kernel()
self.TI_OK = False # Check yourself if OK, then overwrite
if (self._which == 'lowdin'):
assert (self.NOrb == self.mol.nao_nr()
) # Full active space required
ovlp = self.mol.intor_symmetric('int1e_ovlp')
ovlp_eigs, ovlp_vecs = np.linalg.eigh(ovlp)
assert (np.linalg.norm(
np.dot(np.dot(ovlp_vecs, np.diag(ovlp_eigs)), ovlp_vecs.T) -
ovlp) < 1e-10)
self.ao2loc = np.dot(
np.dot(ovlp_vecs, np.diag(np.power(ovlp_eigs, -0.5))),
ovlp_vecs.T)
self.TI_OK = False # Check yourself if OK, then overwrite
if (self._which == 'iao'):
assert (self.NOrb == self.mol.nao_nr()
) # Full active space assumed
self.ao2loc = iao_helper.localize_iao(self.mol, the_mf)
if (ao_rotation is not None):
self.ao2loc = np.dot(self.ao2loc, ao_rotation.T)
self.TI_OK = False # Check yourself if OK, then overwrite
#self.molden( 'dump.molden' ) # Debugging mode
assert (self.loc_ortho() < 1e-9)
'''
# Effective Hamiltonian due to frozen part
self.frozenDMmo = np.array( the_mf.mo_occ, copy=True )
self.frozenDMmo[ self.active==1 ] = 0 # Only the frozen MO occupancies nonzero
self.frozenDMao = np.dot(np.dot( the_mf.mo_coeff, np.diag( self.frozenDMmo )), the_mf.mo_coeff.T )
self.frozenJKao = scf.hf.get_veff( self.mol, self.frozenDMao, 0, 0, 1 ) #Last 3 numbers: dm_last, vhf_last, hermi
self.frozenOEIao = self.fullFOCKao - self.fullJKao + self.frozenJKao
'''
self.frozenOEIao = self.fullOEIao
# Active space OEI and ERI
self.activeCONST = self.mol.energy_nuc(
) #+ np.einsum( 'ij,ij->', self.frozenOEIao - 0.5*self.frozenJKao, self.frozenDMao )
self.activeOEI = np.dot(np.dot(self.ao2loc.T, self.frozenOEIao),
self.ao2loc)
self.activeFOCK = np.dot(np.dot(self.ao2loc.T, self.fullFOCKao),
self.ao2loc)
if (self.NOrb <= 150):
self.ERIinMEM = True
if (self.mol.cart):
intor = 'int2e_cart'
else:
intor = 'int2e_sph'
self.activeERI = ao2mo.outcore.full_iofree(
self.mol, self.ao2loc, intor,
compact=False).reshape(self.NOrb, self.NOrb, self.NOrb,
self.NOrb)
else:
self.ERIinMEM = False
self.activeERI = None
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO,
large_ci_tol=.1, **kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.spheric_labels(True)
if isinstance(ci, (tuple, list)):
ci0 = ci[0]
log.info('** Natural natural orbitals are based on the first root **')
else:
ci0 = ci
if ci0 is None and hasattr(casscf, 'casdm1'):
casdm1 = casscf.casdm1
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
elif hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci0, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci0, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff[:,ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i+1, j+1, s[i,j])
if hasattr(casscf.fcisolver, 'large_ci') and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas)
log.info(' string alpha, string beta, state %d CI coefficient', i)
for c,ia,ib in res:
log.info(' %9s %9s %.12f', ia, ib, c)
else:
log.info(' string alpha, string beta, CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas)
for c,ia,ib in res:
log.info(' %9s %9s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
def analyze(mf,
verbose=logger.DEBUG,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis; Dipole moment
'''
from pyscf.lo import orth
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
nmo = len(mo_occ[0])
log = logger.new_logger(mf, verbose)
if log.verbose >= logger.NOTE:
log.note('**** MO energy ****')
log.note(
' alpha | beta alpha | beta'
)
for i in range(nmo):
log.note('MO #%-3d energy= %-18.15g | %-18.15g occ= %g | %g',
i + MO_BASE, mo_energy[0][i], mo_energy[1][i],
mo_occ[0][i], mo_occ[1][i])
ovlp_ao = mf.get_ovlp()
if log.verbose >= logger.DEBUG:
label = mf.mol.ao_labels()
if with_meta_lowdin:
log.debug(
' ** MO coefficients (expansion on meta-Lowdin AOs) for alpha spin **'
)
orth_coeff = orth.orth_ao(mf.mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
dump_mat.dump_rec(mf.stdout,
c_inv.dot(mo_coeff[0]),
label,
start=MO_BASE,
**kwargs)
log.debug(
' ** MO coefficients (expansion on meta-Lowdin AOs) for beta spin **'
)
dump_mat.dump_rec(mf.stdout,
c_inv.dot(mo_coeff[1]),
label,
start=MO_BASE,
**kwargs)
else:
log.debug(
' ** MO coefficients (expansion on AOs) for alpha spin **')
dump_mat.dump_rec(mf.stdout,
mo_coeff[0],
label,
start=MO_BASE,
**kwargs)
log.debug(
' ** MO coefficients (expansion on AOs) for beta spin **')
dump_mat.dump_rec(mf.stdout,
mo_coeff[1],
label,
start=MO_BASE,
**kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
return (mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
else:
return (mf.mulliken_pop(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
def analyze(mf, verbose=logger.DEBUG, **kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
mol = mf.mol
if not mol.symmetry:
return uhf.analyze(mf, verbose, **kwargs)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
log = logger.Logger(mf.stdout, verbose)
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsyma = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff[0], ovlp_ao, False)
orbsymb = symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff[1], ovlp_ao, False)
orbsyma = numpy.array(orbsyma)
orbsymb = numpy.array(orbsymb)
tot_sym = 0
noccsa = [sum(orbsyma[mo_occ[0]>0]==ir) for ir in mol.irrep_id]
noccsb = [sum(orbsymb[mo_occ[1]>0]==ir) for ir in mol.irrep_id]
for i, ir in enumerate(mol.irrep_id):
if (noccsa[i]+noccsb[i]) % 2:
tot_sym ^= ir
if mol.groupname in ('Dooh', 'Coov', 'SO3'):
log.note('TODO: total symmetry for %s', mol.groupname)
else:
log.note('total symmetry = %s',
symm.irrep_id2name(mol.groupname, tot_sym))
log.note('alpha occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsa)
log.note('beta occupancy for each irrep: '+(' %4s'*nirrep),
*mol.irrep_name)
log.note(' '+(' %4d'*nirrep),
*noccsb)
ss, s = mf.spin_square((mo_coeff[0][:,mo_occ[0]>0],
mo_coeff[1][:,mo_occ[1]>0]), ovlp_ao)
log.note('multiplicity <S^2> = %.8g 2S+1 = %.8g', ss, s)
if verbose >= logger.NOTE:
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('alpha MO #%d (%s #%d), energy= %.15g occ= %g',
k+1, irname_full[j], irorbcnt[j], mo_energy[0][k], mo_occ[0][k])
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('beta MO #%d (%s #%d), energy= %.15g occ= %g',
k+1, irname_full[j], irorbcnt[j], mo_energy[1][k], mo_occ[1][k])
ovlp_ao = mf.get_ovlp()
if mf.verbose >= logger.DEBUG:
label = mol.spheric_labels(True)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** alpha MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c_inv = numpy.dot(orth_coeff.T, ovlp_ao)
dump_mat.dump_rec(mol.stdout, c_inv.dot(mo_coeff[0]), label, molabel,
start=1, **kwargs)
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsymb):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' % (k+1, irname_full[j], irorbcnt[j]))
log.debug(' ** beta MO coefficients (expansion on meta-Lowdin AOs) **')
dump_mat.dump_rec(mol.stdout, c_inv.dot(mo_coeff[1]), label, molabel,
start=1, **kwargs)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
def atomic_pops(mol, mo_coeff, method='meta_lowdin', mf=None):
'''
Kwargs:
method : string
The atomic population projection scheme. It can be mulliken,
lowdin, meta_lowdin, iao, or becke
Returns:
A 3-index tensor [A,i,j] indicates the population of any orbital-pair
density |i><j| for each species (atom in this case). This tensor is
used to construct the population and gradients etc.
You can customize the PM localization wrt other population metric,
such as the charge of a site, the charge of a fragment (a group of
atoms) by overwriting this tensor. See also the example
pyscf/examples/loc_orb/40-hubbard_model_PM_localization.py for the PM
localization of site-based population for hubbard model.
'''
method = method.lower().replace('_', '-')
nmo = mo_coeff.shape[1]
proj = numpy.empty((mol.natm, nmo, nmo))
if getattr(mol, 'pbc_intor', None): # whether mol object is a cell
s = mol.pbc_intor('int1e_ovlp_sph', hermi=1)
else:
s = mol.intor_symmetric('int1e_ovlp')
if method == 'becke':
from pyscf.dft import gen_grid
if not (getattr(mf, 'grids', None) and getattr(mf, '_numint', None)):
# Call DFT to initialize grids and numint objects
mf = mol.RKS()
grids = mf.grids
ni = mf._numint
if not isinstance(grids, gen_grid.Grids):
raise NotImplementedError('PM becke scheme for PBC systems')
# The atom-wise Becke grids (without concatenated to a vector of grids)
coords, weights = grids.get_partition(mol, concat=False)
for i in range(mol.natm):
ao = ni.eval_ao(mol, coords[i], deriv=0)
aow = numpy.einsum('pi,p->pi', ao, weights[i])
charge_matrix = lib.dot(aow.conj().T, ao)
proj[i] = reduce(lib.dot,
(mo_coeff.conj().T, charge_matrix, mo_coeff))
elif method == 'mulliken':
for i, (b0, b1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
csc = reduce(numpy.dot,
(mo_coeff[p0:p1].conj().T, s[p0:p1], mo_coeff))
proj[i] = (csc + csc.conj().T) * .5
elif method in ('lowdin', 'meta-lowdin'):
c = orth.restore_ao_character(mol, 'ANO')
#csc = reduce(lib.dot, (mo_coeff.conj().T, s, orth_local_ao_coeff))
csc = reduce(lib.dot,
(mo_coeff.conj().T, s, orth.orth_ao(mol, method, c, s=s)))
for i, (b0, b1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
proj[i] = numpy.dot(csc[:, p0:p1], csc[:, p0:p1].conj().T)
elif method in ('iao', 'ibo'):
from pyscf.lo import iao
assert mf is not None
# FIXME: How to handle UHF/UKS object?
orb_occ = mf.mo_coeff[:, mf.mo_occ > 0]
iao_coeff = iao.iao(mol, orb_occ)
#
# IAO is generally not orthogonalized. For simplicity, we take Lowdin
# orthogonalization here. Other orthogonalization can be used. Results
# should be very closed to the Lowdin-orth orbitals
#
# PM with Mulliken population of non-orth IAOs can be found in
# ibo.PipekMezey function
#
iao_coeff = orth.vec_lowdin(iao_coeff, s)
csc = reduce(lib.dot, (mo_coeff.conj().T, s, iao_coeff))
iao_mol = iao.reference_mol(mol)
for i, (b0, b1, p0, p1) in enumerate(iao_mol.offset_nr_by_atom()):
proj[i] = numpy.dot(csc[:, p0:p1], csc[:, p0:p1].conj().T)
else:
raise KeyError('method = %s' % method)
return proj
def analyze(self,
verbose=None,
with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
if verbose is None: verbose = self.verbose
from pyscf.lo import orth
from pyscf.tools import dump_mat
if not self.mol.symmetry:
return rohf.ROHF.analyze(self, verbose, with_meta_lowdin, **kwargs)
mol = self.mol
mo_energy = self.mo_energy
mo_occ = self.mo_occ
mo_coeff = self.mo_coeff
ovlp_ao = self.get_ovlp()
log = logger.new_logger(self, verbose)
if log.verbose >= logger.NOTE:
nirrep = len(mol.irrep_id)
orbsym = get_orbsym(self.mol, mo_coeff)
wfnsym = 0
ndoccs = []
nsoccs = []
for k, ir in enumerate(mol.irrep_id):
ndoccs.append(sum(orbsym[mo_occ == 2] == ir))
nsoccs.append(sum(orbsym[mo_occ == 1] == ir))
if nsoccs[k] % 2 == 1:
wfnsym ^= ir
if mol.groupname in ('SO3', 'Dooh', 'Coov'):
log.note('TODO: total wave-function symmetry for %s',
mol.groupname)
else:
log.note('Wave-function symmetry = %s',
symm.irrep_id2name(mol.groupname, wfnsym))
log.note('occupancy for each irrep: ' + (' %4s' * nirrep),
*mol.irrep_name)
log.note('double occ ' + (' %4d' * nirrep),
*ndoccs)
log.note('single occ ' + (' %4d' * nirrep),
*nsoccs)
log.note('**** MO energy ****')
irname_full = {}
for k, ir in enumerate(mol.irrep_id):
irname_full[ir] = mol.irrep_name[k]
irorbcnt = {}
if getattr(mo_energy, 'mo_ea', None) is not None:
mo_ea = mo_energy.mo_ea
mo_eb = mo_energy.mo_eb
log.note(
' Roothaan | alpha | beta'
)
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note(
'MO #%-4d(%-3s #%-2d) energy= %-18.15g | %-18.15g | %-18.15g occ= %g',
k + MO_BASE, irname_full[j], irorbcnt[j], mo_energy[k],
mo_ea[k], mo_eb[k], mo_occ[k])
else:
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.note('MO #%-3d (%s #%-2d), energy= %-18.15g occ= %g',
k + MO_BASE, irname_full[j], irorbcnt[j],
mo_energy[k], mo_occ[k])
if log.verbose >= logger.DEBUG:
label = mol.ao_labels()
molabel = []
irorbcnt = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
molabel.append('#%-d(%s #%d)' %
(k + MO_BASE, irname_full[j], irorbcnt[j]))
if with_meta_lowdin:
log.debug(
' ** MO coefficients (expansion on meta-Lowdin AOs) **')
orth_coeff = orth.orth_ao(mol, 'meta_lowdin', s=ovlp_ao)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
else:
log.debug(' ** MO coefficients (expansion on AOs) **')
c = mo_coeff
dump_mat.dump_rec(self.stdout,
c,
label,
molabel,
start=MO_BASE,
**kwargs)
dm = self.make_rdm1(mo_coeff, mo_occ)
if with_meta_lowdin:
pop_and_charge = self.mulliken_meta(mol,
dm,
s=ovlp_ao,
verbose=log)
else:
pop_and_charge = self.mulliken_pop(mol, dm, s=ovlp_ao, verbose=log)
dip = self.dip_moment(mol, dm, verbose=log)
return pop_and_charge, dip
def analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO,
large_ci_tol=.1, **kwargs):
from pyscf.lo import orth
from pyscf.tools import dump_mat
if mo_coeff is None: mo_coeff = casscf.mo_coeff
if ci is None: ci = casscf.ci
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(casscf.stdout, verbose)
nelecas = casscf.nelecas
ncas = casscf.ncas
ncore = casscf.ncore
nocc = ncore + ncas
label = casscf.mol.ao_labels()
if isinstance(ci, (tuple, list)):
ci0 = ci[0]
log.info('** Natural natural orbitals are based on the first root **')
else:
ci0 = ci
if ci0 is None and hasattr(casscf, 'casdm1'):
casdm1 = casscf.casdm1
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
elif hasattr(casscf.fcisolver, 'make_rdm1s'):
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci0, ncas, nelecas)
casdm1 = casdm1a + casdm1b
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1b = numpy.dot(mocore, mocore.T)
dm1a = dm1b + reduce(numpy.dot, (mocas, casdm1a, mocas.T))
dm1b += reduce(numpy.dot, (mocas, casdm1b, mocas.T))
dm1 = dm1a + dm1b
if log.verbose >= logger.DEBUG1:
log.info('alpha density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1a, label, **kwargs)
log.info('beta density matrix (on AO)')
dump_mat.dump_tri(log.stdout, dm1b, label, **kwargs)
else:
casdm1 = casscf.fcisolver.make_rdm1(ci0, ncas, nelecas)
mocore = mo_coeff[:,:ncore]
mocas = mo_coeff[:,ncore:nocc]
dm1a =(numpy.dot(mocore, mocore.T) * 2
+ reduce(numpy.dot, (mocas, casdm1, mocas.T)))
dm1b = None
dm1 = dm1a
if log.verbose >= logger.INFO:
ovlp_ao = casscf._scf.get_ovlp()
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-casdm1, ncore, nocc)
log.info('Natural occ %s', str(-occ))
for i, k in enumerate(numpy.argmax(abs(ucas), axis=0)):
if ucas[k,i] < 0:
ucas[:,i] *= -1
orth_coeff = orth.orth_ao(casscf.mol, 'meta_lowdin', s=ovlp_ao)
mo_cas = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff[:,ncore:nocc], ucas))
log.info('Natural orbital (expansion on meta-Lowdin AOs) in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1, **kwargs)
if casscf._scf.mo_coeff is not None:
s = reduce(numpy.dot, (casscf.mo_coeff.T, ovlp_ao, casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s)>.4)
for i,j in idx:
log.info('<mo-mcscf|mo-hf> %d %d %12.8f', i+1, j+1, s[i,j])
if hasattr(casscf.fcisolver, 'large_ci') and ci is not None:
log.info('** Largest CI components **')
if isinstance(ci, (tuple, list)):
for i, civec in enumerate(ci):
res = casscf.fcisolver.large_ci(civec, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
log.info(' [alpha occ-orbitals] [beta occ-orbitals] state %-3d CI coefficient', i)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
else:
log.info(' [alpha occ-orbitals] [beta occ-orbitals] CI coefficient')
res = casscf.fcisolver.large_ci(ci, casscf.ncas, casscf.nelecas,
large_ci_tol, return_strs=False)
for c,ia,ib in res:
log.info(' %-20s %-30s %.12f', ia, ib, c)
casscf._scf.mulliken_meta(casscf.mol, dm1, s=ovlp_ao, verbose=log)
return dm1a, dm1b
