def kernel(self, h1e, eri, norb, nelec, ci0=None, **kwargs):
if self.verbose > logger.QUIET:
pyscf.gto.mole.check_sanity(self, self._keys, self.stdout)
wfnsym = _id_wfnsym(self, norb, nelec, self.wfnsym)
if 'verbose' in kwargs:
if isinstance(kwargs['verbose'], logger.Logger):
log = kwargs['verbose']
else:
log = logger.Logger(self.stdout, kwargs['verbose'])
log.debug('total symmetry = %s',
symm.irrep_id2name(self.mol.groupname, wfnsym))
else:
logger.debug(self, 'total symmetry = %s',
symm.irrep_id2name(self.mol.groupname, wfnsym))
e, c = direct_spin1.kernel_ms1(self, h1e, eri, norb, nelec, ci0,
**kwargs)
if self.wfnsym is not None:
# should I remove the non-symmetric contributions in each
# call of contract_2e?
if self.nroots > 1:
c = [addons.symmetrize_wfn(ci, norb, nelec, self.orbsym, wfnsym)
for ci in c]
else:
c = addons.symmetrize_wfn(c, norb, nelec, self.orbsym, wfnsym)
return e, c
def kernel(self, mo_coeff=None, ci0=None, callback=None, _kern=None):
if mo_coeff is None:
mo_coeff = self.mo_coeff
if callback is None: callback = self.callback
if _kern is None: _kern = newton_casscf.kernel
if self.verbose >= logger.WARN:
self.check_sanity()
self.dump_flags()
log = logger.Logger(self.stdout, self.verbose)
mo_coeff = self.mo_coeff = casci_symm.label_symmetry_(self, mo_coeff)
if (hasattr(self.fcisolver, 'wfnsym') and
self.fcisolver.wfnsym is None and
hasattr(self.fcisolver, 'guess_wfnsym')):
wfnsym = self.fcisolver.guess_wfnsym(self.ncas, self.nelecas, ci0,
verbose=log)
wfnsym = symm.irrep_id2name(self.mol.groupname, wfnsym)
log.info('Active space CI wfn symmetry = %s', wfnsym)
self.converged, self.e_tot, self.e_cas, self.ci, \
self.mo_coeff, self.mo_energy = \
_kern(self, mo_coeff,
tol=self.conv_tol, conv_tol_grad=self.conv_tol_grad,
ci0=ci0, callback=callback, verbose=self.verbose)
log.note('CASSCF energy = %.15g', self.e_tot)
self._finalize()
return self.e_tot, self.e_cas, self.ci, self.mo_coeff, self.mo_energy
def kernel(self, mo_coeff=None, ci0=None, callback=None, _kern=None):
if mo_coeff is None:
mo_coeff = self.mo_coeff
else:
self.mo_coeff = mo_coeff
if callback is None: callback = self.callback
if _kern is None: _kern = mc1step.kernel
if self.verbose >= logger.WARN:
self.check_sanity()
self.dump_flags()
log = logger.Logger(self.stdout, self.verbose)
casci_symm.label_symmetry_(self, self.mo_coeff)
if (hasattr(self.fcisolver, 'wfnsym') and
self.fcisolver.wfnsym is None and
hasattr(self.fcisolver, 'guess_wfnsym')):
wfnsym = self.fcisolver.guess_wfnsym(self.ncas, self.nelecas, ci0,
verbose=log)
wfnsym = symm.irrep_id2name(self.mol.groupname, wfnsym)
log.info('Active space CI wfn symmetry = %s', wfnsym)
self.converged, self.e_tot, self.e_cas, self.ci, \
self.mo_coeff, self.mo_energy = \
_kern(self, mo_coeff,
tol=self.conv_tol, conv_tol_grad=self.conv_tol_grad,
ci0=ci0, callback=callback, verbose=self.verbose)
log.note('CASSCF energy = %.15g', self.e_tot)
self._finalize()
return self.e_tot, self.e_cas, self.ci, self.mo_coeff, self.mo_energy
def dump_flags(self, verbose=None):
direct_spin1.FCISolver.dump_flags(self, verbose)
if isinstance(self.wfnsym, str):
logger.info(self, 'specified total symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.integer)):
logger.info(self, 'specified total symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
def analyze(mf, verbose=logger.DEBUG, **kwargs):
mol = mf.mol
if not mol.symmetry:
return ghf.analyze(mf, verbose, **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]
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])
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
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 dump_flags(self, verbose=None):
direct_spin0.FCISolver.dump_flags(self, verbose)
log = logger.new_logger(self, verbose)
if isinstance(self.wfnsym, str):
log.info('specified CI wfn symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.number)):
log.info('specified CI wfn symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
def dump_flags(self, verbose=None):
if verbose is None: verbose = self.verbose
direct_spin0.FCISolver.dump_flags(self, verbose)
log = pyscf.lib.logger.Logger(self.stdout, verbose)
if isinstance(self.wfnsym, str):
log.info('specified CI wfn symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.integer)):
log.info('specified CI wfn symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
def analyze(self, verbose=logger.DEBUG):
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 = {}
for k, j in enumerate(orbsym):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.info('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 **')
dump_mat.dump_rec(mol.stdout, mo_coeff, label, molabel, start=1)
dm = self.make_rdm1(mo_coeff, mo_occ)
return self.mulliken_meta(mol, dm, s=ovlp_ao, verbose=verbose)
def dump_flags(self, verbose=None):
if verbose is None: verbose = self.verbose
direct_spin1.FCISolver.dump_flags(self, verbose)
log = logger.Logger(self.stdout, verbose)
if isinstance(self.wfnsym, str):
log.info('specified CI wfn symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.number)):
log.info('specified CI wfn symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
return self
def get_init_guess(self, norb, nelec, nroots, hdiag_csf):
''' The existing _get_init_guess function will work in the csf basis if I pass it with na, nb = ncsf, 1. This might change in future PySCF versions though.
...For point-group symmetry, I pass the direct_spin1.py version of _get_init_guess with na, nb = ncsf_sym, 1 and hdiag_csf including only csfs of the right point-group symmetry.
This should clean up the symmetry-breaking "noise" in direct_spin0_symm.py! '''
wfnsym = _id_wfnsym(self, norb, nelec, self.orbsym, self.wfnsym)
wfnsym_str = symm.irrep_id2name (self.mol.groupname, wfnsym)
self.check_mask_cache ()
idx_sym = self.confsym[self.econf_csf_mask] == wfnsym
return get_init_guess (norb, nelec, nroots, hdiag_csf, smult=self.smult, csd_mask=self.csd_mask,
wfnsym_str=wfnsym_str, idx_sym=idx_sym)
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 dump_flags(self, verbose=None):
if verbose is None: verbose = self.verbose
direct_spin1.FCISolver.dump_flags(self, verbose)
log = logger.Logger(self.stdout, verbose)
if isinstance(self.wfnsym, str):
log.info('Input CI wfn symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.number)):
log.info('Input CI wfn symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
else:
log.info('CI wfn symmetry = %s', self.wfnsym)
return self
def analyze_wfnsym(tdobj, x_sym, x):
'''Guess the wfn symmetry of TDDFT X amplitude'''
possible_sym = x_sym[(x > 1e-7) | (x < -1e-7)]
if numpy.all(possible_sym == symm.MULTI_IRREPS):
if tdobj.wfnsym is None:
wfnsym = '???'
else:
wfnsym = tdobj.wfnsym
else:
ids = possible_sym[possible_sym != symm.MULTI_IRREPS]
ids = numpy.unique(ids)
if ids.size == 1:
wfnsym = symm.irrep_id2name(tdobj.mol.groupname, ids[0])
else:
wfnsym = '???'
return wfnsym
def dump_flags(self, verbose=None):
direct_spin1.FCISolver.dump_flags(self, verbose)
log = logger.new_logger(self, verbose)
if isinstance(self.wfnsym, str):
log.info('Input CI wfn symmetry = %s', self.wfnsym)
elif isinstance(self.wfnsym, (int, numpy.number)):
try:
log.info('Input CI wfn symmetry = %s',
symm.irrep_id2name(self.mol.groupname, self.wfnsym))
except KeyError:
raise RuntimeError(
'FCISolver cannot find mwfnsym Id %s in group %s. '
'This might be caused by the projection from '
'high-symmetry group to D2h symmetry.' %
(self.wfnsym, self.mol.groupname))
else:
log.info('CI wfn symmetry = %s', self.wfnsym)
return self
def las_symm_tuple(las):
# This really should be much more modular
# Symmetry tuple: neleca, nelecb, irrep
statesym = []
s2_states = []
for iroot in range(las.nroots):
neleca = 0
nelecb = 0
wfnsym = 0
s = 0
m = []
for fcibox, nelec in zip(las.fciboxes, las.nelecas_sub):
solver = fcibox.fcisolvers[iroot]
na, nb = _unpack_nelec(fcibox._get_nelec(solver, nelec))
neleca += na
nelecb += nb
s_frag = (solver.smult - 1) // 2
s += s_frag * (s_frag + 1)
m.append((na - nb) // 2)
fragsym = getattr(solver, 'wfnsym',
0) or 0 # in case getattr returns "None"
if isinstance(fragsym, str):
fragsym = symm.irrep_name2id(solver.mol.groupname, fragsym)
assert isinstance(fragsym, (int, np.integer)), '{} {}'.format(
type(fragsym), fragsym)
wfnsym ^= fragsym
s += sum([2 * m1 * m2 for m1, m2 in combinations(m, 2)])
s2_states.append(s)
statesym.append((neleca, nelecb, wfnsym))
lib.logger.info(las, 'Symmetry analysis of LAS states:')
lib.logger.info(
las, ' {:2s} {:>16s} {:6s} {:6s} {:6s} {:6s}'.format(
'ix', 'Energy', 'Neleca', 'Nelecb', '<S**2>', 'Wfnsym'))
for ix, (e, sy, s2) in enumerate(zip(las.e_states, statesym, s2_states)):
neleca, nelecb, wfnsym = sy
wfnsym = symm.irrep_id2name(las.mol.groupname, wfnsym)
lib.logger.info(
las, ' {:2d} {:16.10f} {:6d} {:6d} {:6.3f} {:>6s}'.format(
ix, e, neleca, nelecb, s2, wfnsym))
return statesym, np.asarray(s2_states)
def analyze(mf, verbose=logger.DEBUG, with_meta_lowdin=WITH_META_LOWDIN,
**kwargs):
mol = mf.mol
if not mol.symmetry:
return ghf.analyze(mf, verbose, **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]
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+MO_BASE, irname_full[j], irorbcnt[j], mo_energy[k],
mo_occ[k])
dm = mf.make_rdm1(mo_coeff, mo_occ)
dip = mf.dip_moment(mol, dm, verbose=log)
if with_meta_lowdin:
pop_and_chg = mf.mulliken_meta(mol, dm, s=ovlp_ao, verbose=log)
else:
pop_and_chg = mf.mulliken_pop(mol, dm, s=ovlp_ao, verbose=log)
return pop_and_chg, dip
def run_FCI(molecule: MolecularData, roots: int):
pyscf_mol = molecule._pyscf_data['mol']
pyscf_scf = molecule._pyscf_data['scf']
pyscf_mol.symmetry = True
pyscf_mol.build()
# label orbital symmetries
orbsym = scf.hf_symm.get_orbsym(pyscf_mol, pyscf_scf.mo_coeff)
pyscf_mol.symmetry = False
# generate FCI solver
fci_solver = fci.addons.fix_spin_(fci.FCI(pyscf_mol, pyscf_scf.mo_coeff),
shift=0.0,
ss=1.0)
fci_solver.nroots = roots
# execute FCI solver
f, d = fci_solver.kernel()
fci_e = []
print(' FCI:')
# iterate over eigenstates
for i, x in enumerate(d):
energy = f[i]
mult = fci.spin_op.spin_square0(x, molecule.n_orbitals,
molecule.n_electrons)[1]
eigen_symm = fci.addons.guess_wfnsym(x, molecule.n_orbitals,
molecule.n_electrons, orbsym)
eigen_symm = symm.irrep_id2name('Coov', eigen_symm)
fci_e.append((energy, mult))
print('state {}, E = {}, 2S+1 = {}, IrRep = {} '.format(
i, round(energy, 5), round(mult), eigen_symm))
return fci_e
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 __init__(self, mol_or_hdf5, c=None, network=None, verbose=None):
'''Initializing the T3NS calculation.
Args:
mol_or_hdf5: An instance of :class:`Mole` from PySCF
or a string to a path of the hdf5 file. In this case c and network
should be left as defaults.
c: The orbital coefficients.
The default are the RHF orbitals.
network: Network of the tensor network.
This can be the string 'DMRG' for a linear chain or 'T3NS' for a
T3NS that is radially extended (i.e. the maximal distance between
two sites is minimal). An instance of :class:`Network` is also
accepted for custom networks or a path to a network file.
Default is 'T3NS' if Mole instance was passed, else None.
'''
from pyscf import symm
if isinstance(mol_or_hdf5, pyscf.gto.Mole):
# Initialize with RHF
mol = mol_or_hdf5
if network is None:
network = 'T3NS'
if verbose is None:
self.verbose = mol.verbose
self.mol = mol
# if no orbital coefficients are given, use RHF orbitals
if c is None:
myhf = pyscf.scf.RHF(mol)
myhf.verbose = self.verbose
myhf.kernel()
c = myhf.mo_coeff
self._c = c
self._mol = mol
self._eri = pyscf.ao2mo.kernel(mol, c)
self.symmetries = ['Z2', 'U1', 'SU2']
self.target = [int(mol.nelectron % 2), mol.nelectron, mol.spin]
try:
irrep_ids = symm.label_orb_symm(mol, mol.irrep_id,
mol.symm_orb, c)
newsym = mol.groupname
if mol.groupname == 'Dooh' or mol.groupname == 'Coov':
newsym = 'D2h' if mol.groupname else 'C2v'
if self.verbose > 1:
print(f'Changed point group from {mol.groupname} to '
f'{newsym}')
# mod 10 needed for translation Coov and Dooh
# See https://sunqm.github.io/pyscf/symm.html
self._pg_irrep = [
symm.irrep_id2name(newsym, int(ii % 10))
for ii in irrep_ids
]
self.symmetries.append(newsym)
self.target.append(symm.irrep_id2name(newsym, 0))
except (ValueError, TypeError):
self._pg_irrep = None
if isinstance(network, netw.Network):
self._netw = network
elif network == 'DMRG' or network == 'T3NS':
isDMRG = network == 'DMRG'
self._netw = netw.Network(c.shape[1], isDMRG=isDMRG)
# exchange matrix
# Kij = numpy.zeros((c.shape[1],) * 2)
# trids = numpy.tril_indices(c.shape[1], 0)
# for el, r, c in zip(self._eri.diagonal(), trids[0], trids[1]):
# Kij[r, c] = el
# Kij[c, r] = el
# cost = self._netw.optimize(Kij)
# if self.verbose >= 2:
# print(f'Optimization Exchange-cost: {cost}')
elif isinstance(network, str):
self._netw = netw.Network()
self._netw.readnetworkfile(network)
else:
raise ValueError(f'{network} is invalid for network')
self._netw.pass_network()
elif isinstance(mol_or_hdf5, str):
# h5path = mol_or_hdf5
if verbose is None:
self.verbose = 1
if c is not None or network is not None:
raise ValueError(
'A hdf5 file does not expect a defined c or network')
raise ValueError('Need to implement hdf5 readin still')
else:
raise ValueError(
'Expects a Mole instance or a path to a hdf5 file')
def caslst_by_irrep(casscf,
mo_coeff,
cas_irrep_nocc,
cas_irrep_ncore=None,
s=None,
base=BASE):
'''Given number of active orbitals for each irrep, return the orbital
indices of active space
Args:
casscf : an :class:`CASSCF` or :class:`CASCI` object
cas_irrep_nocc : list or dict
Number of active orbitals for each irrep. It can be a dict, eg
{'A1': 2, 'B2': 4} to indicate the active space size based on
irrep names, or {0: 2, 3: 4} for irrep Id, or a list [2, 0, 0, 4]
(identical to {0: 2, 3: 4}) in which the list index is served as
the irrep Id.
Kwargs:
cas_irrep_ncore : list or dict
Number of closed shells for each irrep. It can be a dict, eg
{'A1': 6, 'B2': 4} to indicate the closed shells based on
irrep names, or {0: 6, 3: 4} for irrep Id, or a list [6, 0, 0, 4]
(identical to {0: 6, 3: 4}) in which the list index is served as
the irrep Id. If cas_irrep_ncore is not given, the program
will generate a guess based on the lowest :attr:`CASCI.ncore`
orbitals.
s : ndarray
overlap matrix
base : int
0-based (C-like) or 1-based (Fortran-like) caslst
Returns:
A list of orbital indices
Examples:
>>> from pyscf import gto, scf, mcscf
>>> mol = gto.M(atom='N 0 0 0; N 0 0 1', basis='ccpvtz', symmetry=True, verbose=0)
>>> mf = scf.RHF(mol)
>>> mf.kernel()
>>> mc = mcscf.CASSCF(mf, 12, 4)
>>> mcscf.caslst_by_irrep(mc, mf.mo_coeff, {'E1gx':4, 'E1gy':4, 'E1ux':2, 'E1uy':2})
[5, 7, 8, 10, 11, 14, 15, 20, 25, 26, 31, 32]
'''
mol = casscf.mol
log = logger.Logger(casscf.stdout, casscf.verbose)
orbsym = numpy.asarray(scf.hf_symm.get_orbsym(mol, mo_coeff))
ncore = casscf.ncore
irreps = set(orbsym)
if cas_irrep_ncore is not None:
irrep_ncore = {}
for k, v in cas_irrep_ncore.items():
if isinstance(k, str):
irrep_ncore[symm.irrep_name2id(mol.groupname, k)] = v
else:
irrep_ncore[k] = v
ncore_rest = ncore - sum(irrep_ncore.values())
if ncore_rest > 0: # guess core configuration
mask = numpy.ones(len(orbsym), dtype=bool)
for ir in irrep_ncore:
mask[orbsym == ir] = False
core_rest = orbsym[mask][:ncore_rest]
core_rest = dict([(ir, numpy.count_nonzero(core_rest == ir))
for ir in set(core_rest)])
log.info('Given core space %s < casscf core size %d',
cas_irrep_ncore, ncore)
log.info('Add %s to core configuration', core_rest)
irrep_ncore.update(core_rest)
elif ncore_rest < 0:
raise ValueError('Given core space %s > casscf core size %d' %
(cas_irrep_ncore, ncore))
else:
irrep_ncore = dict([(ir, sum(orbsym[:ncore] == ir)) for ir in irreps])
if not isinstance(cas_irrep_nocc, dict):
# list => dict
cas_irrep_nocc = dict([(ir, n) for ir, n in enumerate(cas_irrep_nocc)
if n > 0])
irrep_ncas = {}
for k, v in cas_irrep_nocc.items():
if isinstance(k, str):
irrep_ncas[symm.irrep_name2id(mol.groupname, k)] = v
else:
irrep_ncas[k] = v
ncas_rest = casscf.ncas - sum(irrep_ncas.values())
if ncas_rest > 0:
mask = numpy.ones(len(orbsym), dtype=bool)
# remove core and specified active space
for ir in irrep_ncas:
mask[orbsym == ir] = False
for ir, ncore in irrep_ncore.items():
idx = numpy.where(orbsym == ir)[0]
mask[idx[:ncore]] = False
cas_rest = orbsym[mask][:ncas_rest]
cas_rest = dict([(ir, numpy.count_nonzero(cas_rest == ir))
for ir in set(cas_rest)])
log.info('Given active space %s < casscf active space size %d',
cas_irrep_nocc, casscf.ncas)
log.info('Add %s to active space', cas_rest)
irrep_ncas.update(cas_rest)
elif ncas_rest < 0:
raise ValueError(
'Given active space %s > casscf active space size %d' %
(cas_irrep_nocc, casscf.ncas))
caslst = []
for ir, ncas in irrep_ncas.items():
if ncas > 0:
if ir in irrep_ncore:
nc = irrep_ncore[ir]
else:
nc = 0
no = nc + ncas
idx = numpy.where(orbsym == ir)[0]
caslst.extend(idx[nc:no])
caslst = numpy.sort(numpy.asarray(caslst)) + base
if len(caslst) < casscf.ncas:
raise ValueError('Not enough orbitals found for core %s, cas %s' %
(cas_irrep_ncore, cas_irrep_nocc))
if log.verbose >= logger.INFO:
log.info(
'ncore for each irreps %s',
dict([(symm.irrep_id2name(mol.groupname, k), v)
for k, v in irrep_ncore.items()]))
log.info(
'ncas for each irreps %s',
dict([(symm.irrep_id2name(mol.groupname, k), v)
for k, v in irrep_ncas.items()]))
log.info('(%d-based) caslst = %s', base, caslst)
return caslst
def analyze(tdobj, verbose=None):
log = logger.new_logger(tdobj, verbose)
mol = tdobj.mol
mo_coeff = tdobj._scf.mo_coeff
mo_occ = tdobj._scf.mo_occ
nocc = numpy.count_nonzero(mo_occ == 2)
e_ev = numpy.asarray(tdobj.e) * nist.HARTREE2EV
e_wn = numpy.asarray(tdobj.e) * nist.HARTREE2WAVENUMBER
wave_length = 1e11/e_wn
if tdobj.singlet:
log.note('\n** Singlet excitation energies and oscillator strengths **')
else:
log.note('\n** Triplet excitation energies and oscillator strengths **')
if mol.symmetry:
orbsym = hf_symm.get_orbsym(mol, mo_coeff) % 10
x_sym = (orbsym[mo_occ==0,None] ^ orbsym[mo_occ==2]).ravel()
else:
x_sym = None
f_oscillator = tdobj.oscillator_strength()
for i, ei in enumerate(tdobj.e):
x, y = tdobj.xy[i]
if x_sym is None:
log.note('Excited State %3d: %12.5f eV %9.2f nm f=%.4f',
i+1, e_ev[i], wave_length[i], f_oscillator[i])
else:
wfnsym_id = x_sym[abs(x).argmax()]
wfnsym = symm.irrep_id2name(mol.groupname, wfnsym_id)
log.note('Excited State %3d: %4s %12.5f eV %9.2f nm f=%.4f',
i+1, wfnsym, e_ev[i], wave_length[i], f_oscillator[i])
if log.verbose >= logger.INFO:
o_idx, v_idx = numpy.where(abs(x) > 0.1)
for o, v in zip(o_idx, v_idx):
log.info(' %4d -> %-4d %12.5f',
o+MO_BASE, v+MO_BASE+nocc, x[o,v])
if log.verbose >= logger.INFO:
log.info('\n** Transition electric dipole moments (AU) **')
log.info('state X Y Z Dip. S. Osc.')
trans_dip = tdobj.transition_dipole()
for i, ei in enumerate(tdobj.e):
dip = trans_dip[i]
log.info('%3d %11.4f %11.4f %11.4f %11.4f %11.4f',
i+1, dip[0], dip[1], dip[2], numpy.dot(dip, dip),
f_oscillator[i])
log.info('\n** Transition velocity dipole moments (imaginary part AU) **')
log.info('state X Y Z Dip. S. Osc.')
trans_v = tdobj.transition_velocity_dipole()
f_v = tdobj.oscillator_strength(gauge='velocity', order=0)
for i, ei in enumerate(tdobj.e):
v = trans_v[i]
log.info('%3d %11.4f %11.4f %11.4f %11.4f %11.4f',
i+1, v[0], v[1], v[2], numpy.dot(v, v), f_v[i])
log.info('\n** Transition magnetic dipole moments (AU) **')
log.info('state X Y Z')
trans_m = tdobj.transition_magnetic_dipole()
for i, ei in enumerate(tdobj.e):
m = trans_m[i]
log.info('%3d %11.4f %11.4f %11.4f',
i+1, m[0], m[1], m[2])
return tdobj
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 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:
self.dump_scf_summary(log)
nirrep = len(mol.irrep_id)
orbsym = self.get_orbsym(mo_coeff, self.get_ovlp())
irreps = numpy.asarray(mol.irrep_id)
ndoccs = numpy.count_nonzero(irreps[:,
None] == orbsym[mo_occ == 2],
axis=1)
nsoccs = numpy.count_nonzero(irreps[:,
None] == orbsym[mo_occ == 1],
axis=1)
wfnsym = 0
# wfn symmetry is determined by the odd number of electrons in each irrep
for k in numpy.where(nsoccs % 2 == 1)[0]:
ir_in_d2h = mol.irrep_id[k] % 10 # convert to D2h irreps
wfnsym ^= ir_in_d2h
if mol.groupname in ('SO3', 'Dooh', 'Coov'):
# TODO: check wave function symmetry
log.note('Wave-function symmetry = %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.conj().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(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(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 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(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 caslst_by_irrep(casscf, mo_coeff, cas_irrep_nocc,
cas_irrep_ncore=None, s=None, base=1):
'''Given number of active orbitals for each irrep, return the orbital
indices of active space
Args:
casscf : an :class:`CASSCF` or :class:`CASCI` object
cas_irrep_nocc : list or dict
Number of active orbitals for each irrep. It can be a dict, eg
{'A1': 2, 'B2': 4} to indicate the active space size based on
irrep names, or {0: 2, 3: 4} for irrep Id, or a list [2, 0, 0, 4]
(identical to {0: 2, 3: 4}) in which the list index is served as
the irrep Id.
Kwargs:
cas_irrep_ncore : list or dict
Number of closed shells for each irrep. It can be a dict, eg
{'A1': 6, 'B2': 4} to indicate the closed shells based on
irrep names, or {0: 6, 3: 4} for irrep Id, or a list [6, 0, 0, 4]
(identical to {0: 6, 3: 4}) in which the list index is served as
the irrep Id. If cas_irrep_ncore is not given, the program
will generate a guess based on the lowest :attr:`CASCI.ncore`
orbitals.
s : ndarray
overlap matrix
base : int
0-based (C-like) or 1-based (Fortran-like) caslst
Returns:
A list of orbital indices
Examples:
>>> from pyscf import gto, scf, mcscf
>>> mol = gto.M(atom='N 0 0 0; N 0 0 1', basis='ccpvtz', symmetry=True, verbose=0)
>>> mf = scf.RHF(mol)
>>> mf.kernel()
>>> mc = mcscf.CASSCF(mf, 12, 4)
>>> mcscf.caslst_by_irrep(mc, mf.mo_coeff, {'E1gx':4, 'E1gy':4, 'E1ux':2, 'E1uy':2})
[5, 7, 8, 10, 11, 14, 15, 20, 25, 26, 31, 32]
'''
mol = casscf.mol
log = logger.Logger(casscf.stdout, casscf.verbose)
if s is None:
s = casscf._scf.get_ovlp()
orbsym = symm.label_orb_symm(mol, mol.irrep_id,
mol.symm_orb, mo_coeff, s)
orbsym = numpy.asarray(orbsym)
ncore = casscf.ncore
irreps = set(orbsym)
if cas_irrep_ncore is not None:
irrep_ncore = {}
for k, v in cas_irrep_ncore.items():
if isinstance(k, str):
irrep_ncore[symm.irrep_name2id(mol.groupname, k)] = v
else:
irrep_ncore[k] = v
ncore_rest = casscf.ncore - sum(irrep_ncore.values())
if ncore_rest > 0: # guess core configuration
mask = numpy.ones(len(orbsym), dtype=bool)
for ir in irrep_ncore:
mask[orbsym == ir] = False
core_rest = orbsym[mask][:ncore_rest]
core_rest = dict([(ir, numpy.count_nonzero(core_rest==ir))
for ir in set(core_rest)])
log.info('Given core space %s < casscf core size %d',
cas_irrep_ncore, casscf.ncore)
log.info('Add %s to core configuration', core_rest)
irrep_ncore.update(core_rest)
elif ncore_rest < 0:
raise ValueError('Given core space %s > casscf core size %d'
% (cas_irrep_ncore, casscf.ncore))
else:
irrep_ncore = dict([(ir, sum(orbsym[:ncore]==ir)) for ir in irreps])
if not isinstance(cas_irrep_nocc, dict):
# list => dict
cas_irrep_nocc = dict([(ir, n) for ir,n in enumerate(cas_irrep_nocc)
if n > 0])
irrep_ncas = {}
for k, v in cas_irrep_nocc.items():
if isinstance(k, str):
irrep_ncas[symm.irrep_name2id(mol.groupname, k)] = v
else:
irrep_ncas[k] = v
ncas_rest = casscf.ncas - sum(irrep_ncas.values())
if ncas_rest > 0:
mask = numpy.ones(len(orbsym), dtype=bool)
# remove core and specified active space
for ir in irrep_ncas:
mask[orbsym == ir] = False
for ir, ncore in irrep_ncore.items():
idx = numpy.where(orbsym == ir)[0]
mask[idx[:ncore]] = False
cas_rest = orbsym[mask][:ncas_rest]
cas_rest = dict([(ir, numpy.count_nonzero(cas_rest==ir))
for ir in set(cas_rest)])
log.info('Given active space %s < casscf active space size %d',
cas_irrep_nocc, casscf.ncas)
log.info('Add %s to active space', cas_rest)
irrep_ncas.update(cas_rest)
elif ncas_rest < 0:
raise ValueError('Given active space %s > casscf active space size %d'
% (cas_irrep_nocc, casscf.ncas))
caslst = []
for ir, ncas in irrep_ncas.items():
if ncas > 0:
if ir in irrep_ncore:
nc = irrep_ncore[ir]
else:
nc = 0
no = nc + ncas
idx = numpy.where(orbsym == ir)[0]
caslst.extend(idx[nc:no])
caslst = numpy.sort(numpy.asarray(caslst)) + base
if len(caslst) < casscf.ncas:
raise ValueError('Not enough orbitals found for core %s, cas %s' %
(cas_irrep_ncore, cas_irrep_nocc))
if log.verbose >= logger.INFO:
log.info('ncore for each irreps %s',
dict([(symm.irrep_id2name(mol.groupname, k), v)
for k,v in irrep_ncore.items()]))
log.info('ncas for each irreps %s',
dict([(symm.irrep_id2name(mol.groupname, k), v)
for k,v in irrep_ncas.items()]))
log.info('(%d-based) caslst = %s', base, caslst)
return caslst
def label_symmetry_(mc, mo_coeff, ci0=None):
log = logger.Logger(mc.stdout, mc.verbose)
#irrep_name = mc.mol.irrep_name
irrep_name = mc.mol.irrep_id
s = mc._scf.get_ovlp()
ncore = mc.ncore
nocc = ncore + mc.ncas
try:
orbsym = scf.hf_symm.get_orbsym(mc._scf.mol, mo_coeff, s, True)
except ValueError:
log.warn('mc1step_symm symmetrizes input orbitals')
mo_cor = symm.symmetrize_space(mc.mol, mo_coeff[:, :ncore], s=s, check=False)
mo_act = symm.symmetrize_space(mc.mol, mo_coeff[:,ncore:nocc], s=s, check=False)
mo_vir = symm.symmetrize_space(mc.mol, mo_coeff[:,nocc: ], s=s, check=False)
mo_coeff = numpy.hstack((mo_cor,mo_act,mo_vir))
orbsym = symm.label_orb_symm(mc.mol, irrep_name,
mc.mol.symm_orb, mo_coeff, s=s)
mo_coeff_with_orbsym = lib.tag_array(mo_coeff, orbsym=orbsym)
active_orbsym = getattr(mc.fcisolver, 'orbsym', [])
if (not getattr(active_orbsym, '__len__', None)) or len(active_orbsym) == 0:
mc.fcisolver.orbsym = orbsym[ncore:nocc]
log.debug('Active space irreps %s', str(mc.fcisolver.orbsym))
wfnsym = 0
if getattr(mc.fcisolver, 'wfnsym', None) is not None:
wfnsym = mc.fcisolver.wfnsym
elif ci0 is None:
# Guess wfnsym based on HF determinant. mo_coeff may not be HF
# canonical orbitals. Some checks are needed to ensure that mo_coeff
# are derived from the symmetry adapted SCF calculations.
if mo_coeff is mc._scf.mo_coeff:
wfnsym = 0
for ir in orbsym[mc._scf.mo_occ == 1]:
wfnsym ^= ir
mc.fcisolver.wfnsym = wfnsym
log.debug('Set CASCI wfnsym %s based on HF determinant', wfnsym)
elif getattr(mo_coeff, 'orbsym', None) is not None: # It may be reordered SCF orbitals
cas_orb = mo_coeff[:,ncore:nocc]
s = reduce(numpy.dot, (cas_orb.T, mc._scf.get_ovlp(), mc._scf.mo_coeff))
if numpy.all(numpy.max(s, axis=1) > 1-1e-9):
idx = numpy.argmax(s, axis=1)
cas_orbsym = orbsym[ncore:nocc]
cas_occ = mc._scf.mo_occ[idx]
wfnsym = 0
for ir in cas_orbsym[cas_occ == 1]:
wfnsym ^= ir
mc.fcisolver.wfnsym = wfnsym
log.debug('Active space are constructed from canonical SCF '
'orbitals %s', idx)
log.debug('Set CASCI wfnsym %s based on HF determinant', wfnsym)
elif getattr(mc.fcisolver, 'guess_wfnsym', None):
wfnsym = mc.fcisolver.guess_wfnsym(mc.ncas, mc.nelecas, ci0, verbose=log)
log.debug('CASCI wfnsym %s (based on CI initial guess)', wfnsym)
if isinstance(wfnsym, (int, numpy.integer)):
wfnsym = symm.irrep_id2name(mc.mol.groupname, wfnsym)
log.info('Active space CI wfn symmetry = %s', wfnsym)
return mo_coeff_with_orbsym
def label_symmetry_(mc, mo_coeff, ci0=None):
log = logger.Logger(mc.stdout, mc.verbose)
#irrep_name = mc.mol.irrep_name
irrep_name = mc.mol.irrep_id
s = mc._scf.get_ovlp()
ncore = mc.ncore
nocc = ncore + mc.ncas
try:
orbsym = scf.hf_symm.get_orbsym(mc._scf.mol, mo_coeff, s, True)
except ValueError:
log.warn('mc1step_symm symmetrizes input orbitals')
mo_cor = symm.symmetrize_space(mc.mol,
mo_coeff[:, :ncore],
s=s,
check=False)
mo_act = symm.symmetrize_space(mc.mol,
mo_coeff[:, ncore:nocc],
s=s,
check=False)
mo_vir = symm.symmetrize_space(mc.mol,
mo_coeff[:, nocc:],
s=s,
check=False)
mo_coeff = numpy.hstack((mo_cor, mo_act, mo_vir))
orbsym = symm.label_orb_symm(mc.mol,
irrep_name,
mc.mol.symm_orb,
mo_coeff,
s=s)
mo_coeff_with_orbsym = lib.tag_array(mo_coeff, orbsym=orbsym)
active_orbsym = getattr(mc.fcisolver, 'orbsym', [])
if (not getattr(active_orbsym, '__len__',
None)) or len(active_orbsym) == 0:
mc.fcisolver.orbsym = orbsym[ncore:nocc]
log.info(
'Symmetries of active orbitals: %s', ' '.join([
symm.irrep_id2name(mc.mol.groupname, irrep)
for irrep in mc.fcisolver.orbsym
]))
wfnsym = 0
if getattr(mc.fcisolver, 'wfnsym', None) is not None:
wfnsym = mc.fcisolver.wfnsym
log.debug('Use fcisolver.wfnsym %s', wfnsym)
elif ci0 is None:
# Guess wfnsym based on HF determinant. mo_coeff may not be HF
# canonical orbitals. Some checks are needed to ensure that mo_coeff
# are derived from the symmetry adapted SCF calculations.
if mo_coeff is mc._scf.mo_coeff:
wfnsym = 0
orbsym_in_d2h = numpy.asarray(orbsym) % 10 # convert to D2h irreps
for ir in orbsym_in_d2h[mc._scf.mo_occ == 1]:
wfnsym ^= ir
mc.fcisolver.wfnsym = wfnsym
log.debug('Set CASCI wfnsym %s based on HF determinant', wfnsym)
elif getattr(mo_coeff, 'orbsym',
None) is not None: # It may be reordered SCF orbitals
cas_orb = mo_coeff[:, ncore:nocc]
s = reduce(
numpy.dot,
(cas_orb.conj().T, mc._scf.get_ovlp(), mc._scf.mo_coeff))
if numpy.all(numpy.max(s, axis=1) > 1 - 1e-9):
idx = numpy.argmax(s, axis=1)
cas_orbsym_in_d2h = numpy.asarray(orbsym[ncore:nocc]) % 10
cas_occ = mc._scf.mo_occ[idx]
wfnsym = 0
for ir in cas_orbsym_in_d2h[cas_occ == 1]:
wfnsym ^= ir
mc.fcisolver.wfnsym = wfnsym
log.debug(
'Active space are constructed from canonical SCF '
'orbitals %s', idx)
log.debug('Set CASCI wfnsym %s based on HF determinant',
wfnsym)
elif getattr(mc.fcisolver, 'guess_wfnsym', None):
wfnsym = mc.fcisolver.guess_wfnsym(mc.ncas,
mc.nelecas,
ci0,
verbose=log)
log.debug('CASCI wfnsym %s (based on CI initial guess)', wfnsym)
if isinstance(wfnsym, (int, numpy.integer)):
try:
wfnsym = symm.irrep_id2name(mc.mol.groupname, wfnsym)
except KeyError:
log.warn(
'mwfnsym Id %s not found in group %s. This might be caused by '
'the projection from high-symmetry group to D2h symmetry.',
wfnsym, mc.mol.groupname)
log.info('Active space CI wfn symmetry = %s', wfnsym)
return mo_coeff_with_orbsym
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 hasattr(mo_energy, 'mo_ea'):
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(tdobj, verbose=None):
log = logger.new_logger(tdobj, verbose)
mol = tdobj.mol
mo_coeff = tdobj._scf.mo_coeff
mo_occ = tdobj._scf.mo_occ
nocc = numpy.count_nonzero(mo_occ == 2)
e_ev = numpy.asarray(tdobj.e) * nist.HARTREE2EV
e_wn = numpy.asarray(tdobj.e) * nist.HARTREE2WAVENUMBER
wave_length = 1e11/e_wn
if tdobj.singlet:
log.note('\n** Singlet excitation energies and oscillator strengths **')
else:
log.note('\n** Triplet excitation energies and oscillator strengths **')
if mol.symmetry:
orbsym = hf_symm.get_orbsym(mol, mo_coeff) % 10
x_sym = (orbsym[mo_occ==0,None] ^ orbsym[mo_occ==2]).ravel()
else:
x_sym = None
f_oscillator = tdobj.oscillator_strength()
for i, ei in enumerate(tdobj.e):
x, y = tdobj.xy[i]
if x_sym is None:
log.note('Excited State %3d: %12.5f eV %9.2f nm f=%.4f',
i+1, e_ev[i], wave_length[i], f_oscillator[i])
else:
wfnsym_id = x_sym[abs(x).argmax()]
wfnsym = symm.irrep_id2name(mol.groupname, wfnsym_id)
log.note('Excited State %3d: %4s %12.5f eV %9.2f nm f=%.4f',
i+1, wfnsym, e_ev[i], wave_length[i], f_oscillator[i])
if log.verbose >= logger.INFO:
o_idx, v_idx = numpy.where(abs(x) > 0.1)
for o, v in zip(o_idx, v_idx):
log.info(' %4d -> %-4d %12.5f',
o+MO_BASE, v+MO_BASE+nocc, x[o,v])
if log.verbose >= logger.INFO:
log.info('\n** Transition electric dipole moments (AU) **')
log.info('state X Y Z Dip. S. Osc.')
trans_dip = tdobj.transition_dipole()
for i, ei in enumerate(tdobj.e):
dip = trans_dip[i]
log.info('%3d %11.4f %11.4f %11.4f %11.4f %11.4f',
i+1, dip[0], dip[1], dip[2], numpy.dot(dip, dip),
f_oscillator[i])
log.info('\n** Transition velocity dipole moments (imaginary part AU) **')
log.info('state X Y Z Dip. S. Osc.')
trans_v = tdobj.transition_velocity_dipole()
f_v = tdobj.oscillator_strength(gauge='velocity', order=0)
for i, ei in enumerate(tdobj.e):
v = trans_v[i]
log.info('%3d %11.4f %11.4f %11.4f %11.4f %11.4f',
i+1, v[0], v[1], v[2], numpy.dot(v, v), f_v[i])
log.info('\n** Transition magnetic dipole moments (AU) **')
log.info('state X Y Z')
trans_m = tdobj.transition_magnetic_dipole()
for i, ei in enumerate(tdobj.e):
m = trans_m[i]
log.info('%3d %11.4f %11.4f %11.4f',
i+1, m[0], m[1], m[2])
return tdobj
def analyze(mf, verbose=logger.DEBUG, **kwargs):
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 = 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, **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 lassi(las,
mo_coeff=None,
ci=None,
veff_c=None,
h2eff_sub=None,
orbsym=None,
opt=1):
''' Diagonalize the state-interaction matrix of LASSCF '''
if mo_coeff is None: mo_coeff = las.mo_coeff
if ci is None: ci = las.ci
if orbsym is None:
orbsym = getattr(las.mo_coeff, 'orbsym', None)
if orbsym is None and callable(getattr(las, 'label_symmetry_', None)):
orbsym = las.label_symmetry_(las.mo_coeff).orbsym
if orbsym is not None:
orbsym = orbsym[las.ncore:las.ncore + las.ncas]
o0_memcheck = op_o0.memcheck(las, ci)
if opt == 0 and o0_memcheck == False:
raise RuntimeError('Insufficient memory to use o0 LASSI algorithm')
# Construct second-quantization Hamiltonian
e0, h1, h2 = ham_2q(las, mo_coeff, veff_c=None, h2eff_sub=None)
# Symmetry tuple: neleca, nelecb, irrep
statesym, s2_states = las_symm_tuple(las)
# Loop over symmetry blocks
e_roots = np.zeros(las.nroots, dtype=np.float64)
s2_roots = np.zeros(las.nroots, dtype=np.float64)
si = np.zeros((las.nroots, las.nroots), dtype=np.float64)
s2_mat = np.zeros((las.nroots, las.nroots), dtype=np.float64)
for rootsym in set(statesym):
idx = np.all(np.array(statesym) == rootsym, axis=1)
lib.logger.debug(
las,
'Diagonalizing LAS state symmetry block (neleca, nelecb, irrep) = {}'
.format(rootsym))
if np.count_nonzero(idx) == 1:
lib.logger.debug(las, 'Only one state in this symmetry block')
e_roots[idx] = las.e_states[idx] - e0
si[np.ix_(idx, idx)] = 1.0
s2_roots[idx] = s2_states[idx]
continue
wfnsym = rootsym[-1]
ci_blk = [[c for c, ix in zip(cr, idx) if ix] for cr in ci]
t0 = (time.clock(), time.time())
if (las.verbose > lib.logger.INFO) and (o0_memcheck):
ham_ref, s2_ref, ovlp_ref = op_o0.ham(las,
h1,
h2,
ci_blk,
idx,
orbsym=orbsym,
wfnsym=wfnsym)
t0 = lib.logger.timer(
las,
'LASSI diagonalizer rootsym {} CI algorithm'.format(rootsym),
*t0)
ham_blk, s2_blk, ovlp_blk = op_o1.ham(las,
h1,
h2,
ci_blk,
idx,
orbsym=orbsym,
wfnsym=wfnsym)
t0 = lib.logger.timer(
las,
'LASSI diagonalizer rootsym {} TDM algorithm'.format(rootsym),
*t0)
lib.logger.debug(
las,
'LASSI diagonalizer rootsym {}: ham o0-o1 algorithm disagreement = {}'
.format(rootsym, linalg.norm(ham_blk - ham_ref)))
lib.logger.debug(
las,
'LASSI diagonalizer rootsym {}: S2 o0-o1 algorithm disagreement = {}'
.format(rootsym, linalg.norm(s2_blk - s2_ref)))
lib.logger.debug(
las,
'LASSI diagonalizer rootsym {}: ovlp o0-o1 algorithm disagreement = {}'
.format(rootsym, linalg.norm(ovlp_blk - ovlp_ref)))
errvec = np.concatenate([(ham_blk - ham_ref).ravel(),
(s2_blk - s2_ref).ravel(),
(ovlp_blk - ovlp_ref).ravel()])
if np.amax(np.abs(errvec)) > 1e-8:
raise RuntimeError((
"Congratulations, you have found a bug in either lassi_op_o0 (I really hope not)"
" or lassi_op_o1 (much more likely)!\nPlease inspect the last few printed lines of logger output"
" for more information.\nError in lassi, max abs: {}; norm: {}"
).format(np.amax(np.abs(errvec)), linalg.norm(errvec)))
if opt == 0:
ham_blk = ham_ref
s2_blk = s2_ref
ovlp_blk = ovlp_ref
else:
if (las.verbose > lib.logger.INFO):
lib.logger.debug(
las,
'Insufficient memory to test against o0 LASSI algorithm')
ham_blk, s2_blk, ovlp_blk = op[opt].ham(las,
h1,
h2,
ci_blk,
idx,
orbsym=orbsym,
wfnsym=wfnsym)
t0 = lib.logger.timer(
las, 'LASSI diagonalizer rootsym {}'.format(rootsym), *t0)
lib.logger.debug(las, 'Block Hamiltonian - ecore:')
lib.logger.debug(las, '{}'.format(ham_blk))
lib.logger.debug(las, 'Block S**2:')
lib.logger.debug(las, '{}'.format(s2_blk))
lib.logger.debug(las, 'Block overlap matrix:')
lib.logger.debug(las, '{}'.format(ovlp_blk))
s2_mat[np.ix_(idx, idx)] = s2_blk
diag_test = np.diag(ham_blk)
diag_ref = las.e_states[idx] - e0
lib.logger.debug(
las, '{:>13s} {:>13s} {:>13s}'.format('Diagonal', 'Reference',
'Error'))
for ix, (test, ref) in enumerate(zip(diag_test, diag_ref)):
lib.logger.debug(
las,
'{:13.6e} {:13.6e} {:13.6e}'.format(test, ref, test - ref))
assert (
np.allclose(diag_test, diag_ref, atol=1e-5)
), 'SI Hamiltonian diagonal element error. Inadequate convergence?'
e, c = linalg.eigh(ham_blk, b=ovlp_blk)
s2_blk = c.conj().T @ s2_blk @ c
lib.logger.debug(las, 'Block S**2 in adiabat basis:')
lib.logger.debug(las, '{}'.format(s2_blk))
e_roots[idx] = e
s2_roots[idx] = np.diag(s2_blk)
si[np.ix_(idx, idx)] = c
idx = np.argsort(e_roots)
rootsym = np.array(statesym)[idx]
e_roots = e_roots[idx] + e0
s2_roots = s2_roots[idx]
nelec_roots = [statesym[ix][0:2] for ix in idx]
wfnsym_roots = [statesym[ix][2] for ix in idx]
si = si[:, idx]
si = tag_array(si,
s2=s2_roots,
s2_mat=s2_mat,
nelec=nelec_roots,
wfnsym=wfnsym_roots)
lib.logger.info(las, 'LASSI eigenvalues:')
lib.logger.info(
las, ' {:2s} {:>16s} {:6s} {:6s} {:6s} {:6s}'.format(
'ix', 'Energy', 'Neleca', 'Nelecb', '<S**2>', 'Wfnsym'))
for ix, (er, s2r, rsym) in enumerate(zip(e_roots, s2_roots, rootsym)):
neleca, nelecb, wfnsym = rsym
wfnsym = symm.irrep_id2name(las.mol.groupname, wfnsym)
lib.logger.info(
las, ' {:2d} {:16.10f} {:6d} {:6d} {:6.3f} {:>6s}'.format(
ix, er, neleca, nelecb, s2r, wfnsym))
return e_roots, si
