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, 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 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.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 + 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 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 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)