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 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 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
