def analyze(mf, verbose=logger.DEBUG):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis
'''
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.info('**** MO energy ****')
for i in range(len(mo_energy)):
if mo_occ[i] > 0:
log.info('occupied MO #%d energy= %.15g occ= %g',
i+1, mo_energy[i], mo_occ[i])
else:
log.info('virtual MO #%d energy= %.15g occ= %g',
i+1, mo_energy[i], mo_occ[i])
if verbose >= logger.DEBUG:
log.debug(' ** MO coefficients **')
label = ['%d%3s %s%-4s' % x for x in mf.mol.spheric_labels()]
dump_mat.dump_rec(mf.stdout, mo_coeff, label, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_pop(mf.mol, dm, mf.get_ovlp(), log)
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, **kwargs):
from pyscf.tools import dump_mat
log = logger.new_logger(mf, verbose)
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
log.info('**** MO energy ****')
for i in range(len(mo_energy)):
if mo_occ[i] > 0:
log.info('occupied MO #%d energy= %.15g occ= %g', \
i+1, mo_energy[i], mo_occ[i])
else:
log.info('virtual MO #%d energy= %.15g occ= %g', \
i+1, mo_energy[i], mo_occ[i])
mol = mf.mol
if mf.verbose >= logger.DEBUG1:
log.debug(' ** MO coefficients of large component of postive state (real part) **')
label = mol.spinor_labels()
n2c = mo_coeff.shape[0] // 2
dump_mat.dump_rec(mf.stdout, mo_coeff[n2c:,:n2c].real, label, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
pop_chg = mf.mulliken_pop(mol, dm, mf.get_ovlp(), log)
dip = mf.dip_moment(mol, dm, verbose=log)
return pop_chg, dip
def analyze(mf, verbose=logger.DEBUG):
"""Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Mulliken population analysis
"""
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
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.info("multiplicity <S^2> = %.8g 2S+1 = %.8g", ss, s)
log.info("**** MO energy ****")
for i in range(mo_energy[0].__len__()):
if mo_occ[0][i] > 0:
log.info("alpha occupied MO #%d energy = %.15g occ= %g", i + 1, mo_energy[0][i], mo_occ[0][i])
else:
log.info("alpha virtual MO #%d energy = %.15g occ= %g", i + 1, mo_energy[0][i], mo_occ[0][i])
for i in range(mo_energy[1].__len__()):
if mo_occ[1][i] > 0:
log.info("beta occupied MO #%d energy = %.15g occ= %g", i + 1, mo_energy[1][i], mo_occ[1][i])
else:
log.info("beta virtual MO #%d energy = %.15g occ= %g", i + 1, mo_energy[1][i], mo_occ[1][i])
if mf.verbose >= logger.DEBUG:
log.debug(" ** MO coefficients for alpha spin **")
label = mf.mol.spheric_labels(True)
dump_mat.dump_rec(mf.stdout, mo_coeff[0], label, start=1)
log.debug(" ** MO coefficients for beta spin **")
dump_mat.dump_rec(mf.stdout, mo_coeff[1], label, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_meta(mf.mol, dm, s=mf.get_ovlp(), 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 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 analyze(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
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
casdm1a, casdm1b = casscf.fcisolver.make_rdm1s(ci, ncas, nelecas)
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))
if log.verbose >= logger.INFO:
label = ['%d%3s %s%-4s' % x for x in casscf.mol.spheric_labels()]
if log.verbose >= logger.DEBUG:
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)
# note the last two args of ._eig for mc1step_symm
occ, ucas = casscf._eig(-(casdm1a+casdm1b), 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
mo_cas = numpy.dot(mo_coeff[:,ncore:nocc], ucas)
log.info('Natural orbital in CAS space')
dump_mat.dump_rec(log.stdout, mo_cas, label, start=1)
s = reduce(numpy.dot, (casscf.mo_coeff.T, casscf._scf.get_ovlp(),
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])
log.info('** Largest CI components **')
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)
dm1 = dm1a + dm1b
s = casscf._scf.get_ovlp()
casscf._scf.mulliken_pop(casscf.mol, dm1, s, verbose=log)
casscf._scf.mulliken_pop_meta_lowdin_ao(casscf.mol, dm1, verbose=log)
return dm1a, dm1b
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):
'''Analyze the given SCF object: print orbital energies, occupancies;
print orbital coefficients; Occupancy for each irreps; Mulliken population analysis
'''
from pyscf.tools import dump_mat
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
mo_coeff = mf.mo_coeff
log = pyscf.lib.logger.Logger(mf.stdout, verbose)
mol = mf.mol
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsym = pyscf.symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff, s=ovlp_ao)
orbsym = numpy.array(orbsym)
tot_sym = 0
noccs = [sum(orbsym[mo_occ>0]==ir) for ir in mol.irrep_id]
log.info('total symmetry = %s',
pyscf.symm.irrep_name(mol.groupname, tot_sym))
log.info('occupancy for each irrep: ' + (' %4s'*nirrep), *mol.irrep_name)
log.info('double occ ' + (' %4d'*nirrep), *noccs)
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 = ['%d%3s %s%-4s' % x for x in mol.spheric_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 **')
dump_mat.dump_rec(mol.stdout, mo_coeff, label, molabel, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_pop(mol, dm, ovlp_ao, 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 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(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
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 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)
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])
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(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 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=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 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.mcscf import mc_ao2mo
from pyscf.tools import dump_mat
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]
if hasattr(mc, "orbsym"): # for casci_symm
mc.orbsym[ncore:nocc] = mc.orbsym[ncore:nocc][idx]
mc.fcisolver.orbsym = mc.orbsym[ncore:nocc]
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 in CAS space")
label = mc.mol.spheric_labels(True)
dump_mat.dump_rec(log.stdout, mo_coeff1[:, ncore:nocc], 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) > 0.4)
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 * 0.5, 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(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, RANGE_TYPE)) 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, (list, tuple, RANGE_TYPE)):
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 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;
Spin density for AOs and atoms;
'''
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:
mf.dump_scf_summary(log)
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.conj().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:
log.note(
"\nTo work with the spin densities directly, `use mulliken_meta_spin()` only printing them here.\n"
)
mulliken_meta_spin(mf.mol, dm, s=ovlp_ao, verbose=log)
return (mf.mulliken_meta(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
else:
log.note(
"\nTo work with the spin densities directly, `use mulliken_spin_pop()` only printing them here.\n"
)
mulliken_spin_pop(mf.mol, dm, s=ovlp_ao, verbose=log)
return (mf.mulliken_pop(mf.mol, dm, s=ovlp_ao, verbose=log),
mf.dip_moment(mf.mol, dm, verbose=log))
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
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
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.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(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 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.')
log.debug2(
' ** CASCI/CASSCF orbital coefficients (expansion on meta-Lowdin AOs) **'
)
c = reduce(numpy.dot, (orth_coeff.T, ovlp_ao, mo_coeff))
dump_mat.dump_rec(log.stdout, c, 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
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)
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:
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 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 + 1, 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 + 1, 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 + 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 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
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 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._scf.energy_nuc()
ecore += numpy.einsum('ij,ji', hcore, dm_core)
h1eff = reduce(numpy.dot, (mocas.T, hcore, mocas))
if eris is not None and hasattr(eris, 'ppaa'):
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:
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 hasattr(mo_coeff1, 'orbsym') and sort:
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 = %.12g', e)
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(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 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 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 cas_natorb(mc, mo_coeff=None, ci=None, eris=None, sort=False,
verbose=None):
'''Transform active orbitals to natrual orbitals, and update the CI wfn
Args:
mc : a CASSCF/CASCI object or RHF object
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.mcscf import mc_ao2mo
from pyscf.tools import dump_mat
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
if eris is None: eris = mc_ao2mo._ERIS(mc, mo_coeff, approx=2)
ncore = mc.ncore
ncas = mc.ncas
nocc = ncore + ncas
nelecas = mc.nelecas
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]
if hasattr(mc, 'orbsym'): # for casci_symm
mc.orbsym[ncore:nocc] = mc.orbsym[ncore:nocc][idx]
mc.fcisolver.orbsym = mc.orbsym[ncore:nocc]
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]
ci0 = fci.addons.reorder(ci, nelecas, where_natorb)
# 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 in CAS space')
label = ['%d%3s %s%-4s' % x for x in mc.mol.spheric_labels()]
dump_mat.dump_rec(log.stdout, mo_coeff1[:,ncore:nocc], label, start=1)
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])
h1eff =(reduce(numpy.dot, (mo_coeff[:,ncore:nocc].T, mc.get_hcore(),
mo_coeff[:,ncore:nocc]))
+ eris.vhf_c[ncore:nocc,ncore:nocc])
h1eff = reduce(numpy.dot, (ucas.T, h1eff, ucas))
aaaa = eris.aapp[:,:,ncore:nocc,ncore:nocc].copy()
aaaa = ao2mo.incore.full(ao2mo.restore(8, aaaa, ncas), ucas)
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=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(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(casscf, mo_coeff=None, ci=None, verbose=logger.INFO):
from pyscf.tools import dump_mat
from pyscf.mcscf import addons
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:
# 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
mo_cas = numpy.dot(mo_coeff[:, ncore:nocc], ucas)
log.info("Natural orbital 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, casscf._scf.get_ovlp(), casscf._scf.mo_coeff))
idx = numpy.argwhere(abs(s) > 0.4)
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:
log.info("** Largest CI components **")
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)
s = casscf._scf.get_ovlp()
# casscf._scf.mulliken_pop(casscf.mol, dm1, s, verbose=log)
casscf._scf.mulliken_pop_meta_lowdin_ao(casscf.mol, dm1, verbose=log)
return dm1a, dm1b
def guess_cas(mf, dm, baslst, nelec_tol=.05, occ_cutoff=1e-6, base=0,
orth_method='meta_lowdin', s=None, verbose=None):
'''Using DMET to produce CASSCF initial guess. Return the active space
size, num active electrons and the orbital initial guess.
'''
from pyscf import lo
mol = mf.mol
if isinstance(verbose, logger.Logger):
log = verbose
elif verbose is not None:
log = logger.Logger(mol.stdout, verbose)
else:
log = logger.Logger(mol.stdout, mol.verbose)
if not (isinstance(dm, numpy.ndarray) and dm.ndim == 2): # ROHF/UHF DM
dm = sum(dm)
if base != 0:
baslst = [i-base for i in baslst]
if s is None:
s = mf.get_ovlp()
nao = dm.shape[0]
nimp = len(baslst)
log.debug('*** decompose density matrix')
log.debug('orth AO method = %s', orth_method)
log.debug('embedding AO list = %s', str(baslst))
if orth_method is not None:
corth = lo.orth.orth_ao(mol, method=orth_method, s=s)
cinv = numpy.dot(corth.T, s)
dm = reduce(numpy.dot, (cinv, dm, cinv.T))
else:
corth = numpy.eye(nao)
baslst = numpy.asarray(baslst)
notimp = numpy.asarray([i for i in range(nao) if i not in baslst])
occi, ui = scipy.linalg.eigh(-dm[baslst[:,None],baslst])
occi *= -1
idxi = numpy.argsort(abs(occi-1))
log.debug('entanglement weight occ = %s', str(occi[idxi]))
occb, ub = scipy.linalg.eigh(dm[notimp[:,None],notimp])
idxb = numpy.argsort(abs(occb-1)) # sort by entanglement
occb = occb[idxb]
ub = ub[:,idxb]
# guess ncas and nelecas
nb = ((occb > occ_cutoff) & (occb < 2-occ_cutoff)).sum()
log.debug('bath weight occ = %s', occb[:nb])
cum_nelec = numpy.cumsum(occb[:nb]) + occi.sum()
cum_nelec = numpy.append(occi.sum(), cum_nelec)
log.debug('Active space cum nelec imp|[baths] = %f |%s',
cum_nelec[0], cum_nelec[1:])
ne_error = abs(cum_nelec.round() - cum_nelec)
nb4cas = nb
for i in range(nb):
if (ne_error[i] < nelec_tol and
# whether all baths next to ith bath are less important
(occb[i] < nelec_tol or occb[i] > 2-nelec_tol)):
nb4cas = i
break
ncas = nb4cas + nimp
nelecas = int(cum_nelec[nb4cas].round())
ncore = (mol.nelectron - nelecas) // 2
log.info('From DMET guess, ncas = %d nelecas = %d ncore = %d',
ncas, nelecas, ncore)
if log.verbose >= logger.DEBUG:
log.debug('DMET impurity and bath orbitals on orthogonal AOs')
log.debug('DMET %d impurity sites/occ', nimp)
label = mol.spheric_labels(True)
occ_label = ['#%d/%.5f'%(i+1,x) for i,x in enumerate(occi)]
#dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,baslst], ui),
# label=label, label2=occ_label, start=1)
dump_mat.dump_rec(mol.stdout, ui, label=[label[i] for i in baslst],
label2=occ_label, start=1)
log.debug('DMET %d entangled baths/occ', nb)
occ_label = ['#%d/%.5f'%(i+1,occb[i]) for i in range(nb)]
#dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,notimp], ub[:,:nb]),
# label=label, label2=occ_label, start=1)
dump_mat.dump_rec(mol.stdout, ub[:,:nb], label=[label[i] for i in notimp],
label2=occ_label, start=1)
mob = numpy.dot(corth[:,notimp], ub[:,:nb4cas])
idxenv = numpy.argsort(-occb[nb4cas:]) + nb4cas
mo_env = numpy.dot(corth[:,notimp], ub[:,idxenv])
mocore = mo_env[:,:ncore]
mocas = numpy.hstack((numpy.dot(corth[:,baslst],ui), mob))
movir = mo_env[:,ncore:]
def search_for_degeneracy(e):
idx = numpy.where(abs(e[1:] - e[:-1]) < 1e-6)[0]
return numpy.unique(numpy.hstack((idx, idx+1)))
def symmetrize(e, c):
if mol.symmetry:
degidx = search_for_degeneracy(e)
log.debug1('degidx %s', degidx)
if degidx.size > 0:
esub = e[degidx]
csub = c[:,degidx]
scsub = numpy.dot(s, csub)
emin = abs(esub).min() * .5
es = []
cs = []
for i,ir in enumerate(mol.irrep_id):
so = mol.symm_orb[i]
sosc = numpy.dot(so.T, scsub)
s_ir = reduce(numpy.dot, (so.T, s, so))
fock_ir = numpy.dot(sosc*esub, sosc.T)
e, u = scipy.linalg.eigh(fock_ir, s_ir)
idx = abs(e) > emin
es.append(e[idx])
cs.append(numpy.dot(mol.symm_orb[i], u[:,idx]))
es = numpy.hstack(es)
idx = numpy.argsort(es)
assert(numpy.allclose(es[idx], esub))
c[:,degidx] = numpy.hstack(cs)[:,idx]
return c
if mf.mo_energy is None or mf.mo_coeff is None:
fock = mf.get_hcore()
else:
if isinstance(mf.mo_coeff, numpy.ndarray) and mf.mo_coeff.ndim == 2:
sc = numpy.dot(s, mf.mo_coeff)
fock = numpy.dot(sc*mf.mo_energy, sc.T)
else:
sc = numpy.dot(s, mf.mo_coeff[0])
fock = numpy.dot(sc*mf.mo_energy[0], sc.T)
mo = []
for c in (mocore, mocas, movir):
f1 = reduce(numpy.dot, (c.T, fock, c))
e, u = scipy.linalg.eigh(f1)
log.debug1('Fock eig %s', e)
mo.append(symmetrize(e, numpy.dot(c, u)))
mo = numpy.hstack(mo)
return ncas, nelecas, mo
def kernel(mf, dm, aolabels_or_baslst, nelec_tol=.05, occ_cutoff=1e-6, base=0,
orth_method='meta_lowdin', s=None, canonicalize=True,
freeze_imp=False, verbose=None):
'''DMET method to generate CASSCF initial guess.
Ref. arXiv:1701.07862 [physics.chem-ph]
Args:
mf : an :class:`SCF` object
dm : 2D np.array or a list of 2D array
Density matrix
aolabels_or_baslst : string or a list of strings or a list of index
AO labels or indices
Kwargs:
nelec_tol : float
Entanglement threshold of DMET bath. If the occupancy of an
orbital is less than nelec_tol, the orbital is considered as bath
orbtial. If occ is greater than (1-nelec_tol), the orbitals are
taken for core determinant.
base : int
0-based (C-style) or 1-based (Fortran-style) for baslst if baslst
is index list
orth_method : str
It can be one of 'lowdin' and 'meta_lowdin'
s : 2D array
AO overlap matrix. This option is mainly used for custom Hamilatonian.
canonicalize : bool
Orbitals defined in AVAS method are local orbitals. Symmetrizing
the core, active and virtual space.
Returns:
active-space-size, #-active-electrons, orbital-initial-guess-for-CASCI/CASSCF
Examples:
>>> from pyscf import gto, scf, mcscf
>>> from pyscf.mcscf import dmet_cas
>>> mol = gto.M(atom='Cr 0 0 0; Cr 0 0 1.6', basis='ccpvtz')
>>> mf = scf.RHF(mol).run()
>>> ncas, nelecas, mo = dmet_cas.dmet_cas(mf, ['Cr 3d', 'Cr 4s'])
>>> mc = mcscf.CASSCF(mf, ncas, nelecas).run(mo)
'''
from pyscf import lo
if isinstance(verbose, logger.Logger):
log = verbose
elif verbose is not None:
log = logger.Logger(mf.stdout, verbose)
else:
log = logger.Logger(mf.stdout, mf.verbose)
if not (isinstance(dm, numpy.ndarray) and dm.ndim == 2): # ROHF/UHF DM
dm = sum(dm)
mol = mf.mol
if isinstance(aolabels_or_baslst, str):
baslst = [i for i,t in enumerate(mol.spherical_labels(1))
if aolabels_or_baslst in t]
elif isinstance(aolabels_or_baslst[0], str):
baslst = [i for i,t in enumerate(mol.spherical_labels(1))
if any(x in t for x in aolabels_or_baslst)]
else:
baslst = aolabels_or_baslst
baslst = numpy.asarray(baslst)
if base != 0:
baslst = [i-base for i in baslst]
if s is None:
s = mf.get_ovlp()
if (not isinstance(mf, scf.hf.SCF)) and hasattr(mf, '_scf'):
mf = mf._scf
nao = dm.shape[0]
nimp = len(baslst)
log.debug('*** decompose density matrix')
log.debug('orth AO method = %s', orth_method)
log.debug('embedding AO list = %s', str(baslst))
if orth_method is not None:
corth = lo.orth.orth_ao(mol, method=orth_method, s=s)
cinv = numpy.dot(corth.T, s)
dm = reduce(numpy.dot, (cinv, dm, cinv.T))
else:
corth = numpy.eye(nao)
baslst = numpy.asarray(baslst)
notimp = numpy.asarray([i for i in range(nao) if i not in baslst])
occi, ui = scipy.linalg.eigh(-dm[baslst[:,None],baslst])
occi *= -1
idxi = numpy.argsort(abs(occi-1))
log.debug('entanglement weight occ = %s', str(occi[idxi]))
occb, ub = scipy.linalg.eigh(dm[notimp[:,None],notimp])
idxb = numpy.argsort(abs(occb-1)) # sort by entanglement
occb = occb[idxb]
ub = ub[:,idxb]
# guess ncas and nelecas
nb = ((occb > occ_cutoff) & (occb < 2-occ_cutoff)).sum()
log.debug('bath weight occ = %s', occb[:nb])
cum_nelec = numpy.cumsum(occb[:nb]) + occi.sum()
cum_nelec = numpy.append(occi.sum(), cum_nelec)
log.debug('Active space cum nelec imp|[baths] = %f |%s',
cum_nelec[0], cum_nelec[1:])
ne_error = abs(cum_nelec.round() - cum_nelec)
nb4cas = nb
for i in range(nb):
if (ne_error[i] < nelec_tol and
# whether all baths next to ith bath are less important
(occb[i] < nelec_tol or occb[i] > 2-nelec_tol)):
nb4cas = i
break
ncas = nb4cas + nimp
nelecas = int(cum_nelec[nb4cas].round())
ncore = (mol.nelectron - nelecas) // 2
log.info('From DMET guess, ncas = %d nelecas = %d ncore = %d',
ncas, nelecas, ncore)
log.debug('DMET impurity and bath orbitals on orthogonal AOs')
log.debug('DMET %d impurity sites/occ', nimp)
if log.verbose >= logger.DEBUG1:
label = mol.spherical_labels(True)
occ_label = ['#%d/%.5f'%(i+1,x) for i,x in enumerate(occi)]
#dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,baslst], ui),
# label=label, label2=occ_label, start=1)
dump_mat.dump_rec(mol.stdout, ui, label=[label[i] for i in baslst],
label2=occ_label, start=1)
log.debug('DMET %d entangled baths/occ', nb)
if log.verbose >= logger.DEBUG1:
occ_label = ['#%d/%.5f'%(i+1,occb[i]) for i in range(nb)]
#dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,notimp], ub[:,:nb]),
# label=label, label2=occ_label, start=1)
dump_mat.dump_rec(mol.stdout, ub[:,:nb], label=[label[i] for i in notimp],
label2=occ_label, start=1)
mob = numpy.dot(corth[:,notimp], ub[:,:nb4cas])
idxenv = numpy.argsort(-occb[nb4cas:]) + nb4cas
mo_env = numpy.dot(corth[:,notimp], ub[:,idxenv])
mocore = mo_env[:,:ncore]
mocas = numpy.hstack((numpy.dot(corth[:,baslst],ui), mob))
movir = mo_env[:,ncore:]
if canonicalize or freeze_imp:
if mf.mo_energy is None or mf.mo_coeff is None:
fock = mf.get_hcore()
else:
if isinstance(mf.mo_coeff, numpy.ndarray) and mf.mo_coeff.ndim == 2:
sc = numpy.dot(s, mf.mo_coeff)
fock = numpy.dot(sc*mf.mo_energy, sc.T)
else:
sc = numpy.dot(s, mf.mo_coeff[0])
fock = numpy.dot(sc*mf.mo_energy[0], sc.T)
def trans(c):
if c.shape[1] == 0:
return c
else:
f1 = reduce(numpy.dot, (c.T, fock, c))
e, u = scipy.linalg.eigh(f1)
log.debug1('Fock eig %s', e)
return symmetrize(mol, e, numpy.dot(c, u), s, log)
if freeze_imp:
log.debug('Semi-canonicalization for freeze_imp=True')
mo = numpy.hstack([trans(mocore), trans(mocas[:,:nimp]),
trans(mocas[:,nimp:]), trans(movir)])
else:
mo = numpy.hstack([trans(mocore), trans(mocas), trans(movir)])
else:
mo = numpy.hstack((mocore, mocas, movir))
return ncas, nelecas, mo
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 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(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:
mf.dump_scf_summary(log)
nirrep = len(mol.irrep_id)
orbsym = mf.get_orbsym(mo_coeff, ovlp_ao)
wfnsym = 0
noccs = [sum(orbsym[mo_occ>0]==ir) for ir in mol.irrep_id]
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(' ' + (' %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.conj().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.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 = pyscf.symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb,
mo_coeff[0], s=ovlp_ao)
orbsymb = pyscf.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 ir in range(nirrep):
if (noccsa[ir]+noccsb[ir]) % 2:
tot_sym ^= mol.irrep_id[ir]
if mol.groupname in ('Dooh', 'Coov'):
log.info('TODO: total symmetry for %s', mol.groupname)
else:
log.info('total symmetry = %s', \
pyscf.symm.irrep_name(mol.groupname, tot_sym))
log.info('alpha occupancy for each irrep: '+(' %4s'*nirrep), \
*mol.irrep_name)
log.info(' '+(' %4d'*nirrep), \
*noccsa)
log.info('beta occupancy for each irrep: '+(' %4s'*nirrep), \
*mol.irrep_name)
log.info(' '+(' %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.info('multiplicity <S^2> = %.8g, 2S+1 = %.8g', ss, s)
if verbose >= logger.INFO:
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(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.info('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.info('beta MO #%d (%s #%d), energy= %.15g occ= %g', \
k+1, irname_full[j], irorbcnt[j], mo_energy[1][k], mo_occ[1][k])
if mf.verbose >= logger.DEBUG:
label = ['%d%3s %s%-4s' % x for x in mol.spheric_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 **')
dump_mat.dump_rec(mol.stdout, 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 **')
dump_mat.dump_rec(mol.stdout, mo_coeff[1], label, molabel, start=1)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return mf.mulliken_pop(mol, dm, ovlp_ao, log)
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(mf, verbose=logger.DEBUG):
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 = pyscf.symm.label_orb_symm(mol, mol.irrep_id, mol.symm_orb, mo_coeff[0], s=ovlp_ao)
orbsymb = pyscf.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 ir in range(nirrep):
if (noccsa[ir] + noccsb[ir]) % 2:
tot_sym ^= mol.irrep_id[ir]
if mol.groupname in ("Dooh", "Coov", "SO3"):
log.info("TODO: total symmetry for %s", mol.groupname)
else:
log.info("total symmetry = %s", pyscf.symm.irrep_id2name(mol.groupname, tot_sym))
log.info("alpha occupancy for each irrep: " + (" %4s" * nirrep), *mol.irrep_name)
log.info(" " + (" %4d" * nirrep), *noccsa)
log.info("beta occupancy for each irrep: " + (" %4s" * nirrep), *mol.irrep_name)
log.info(" " + (" %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.info("multiplicity <S^2> = %.8g 2S+1 = %.8g", ss, s)
if verbose >= logger.INFO:
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(orbsyma):
if j in irorbcnt:
irorbcnt[j] += 1
else:
irorbcnt[j] = 1
log.info(
"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.info(
"beta MO #%d (%s #%d), energy= %.15g occ= %g",
k + 1,
irname_full[j],
irorbcnt[j],
mo_energy[1][k],
mo_occ[1][k],
)
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 **")
dump_mat.dump_rec(mol.stdout, 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 **")
dump_mat.dump_rec(mol.stdout, 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):
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 _decompose_dm(mol, dm, baslst, ncas, nelecas, ncore, occ_cutoff=1e-8,
baths=None, base=1, orth_method='meta_lowdin', s=None,
verbose=logger.WARN):
from pyscf import lo
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
assert(isinstance(dm, numpy.ndarray) and dm.ndim == 2)
if base != 0:
baslst = [i-base for i in baslst]
nao = dm.shape[0]
nocc = ncore + ncas
nimp = len(baslst)
log.debug('*** decompose density matrix')
log.debug('orth AO method = %s', orth_method)
log.debug('embedding AO list = %s', str(baslst))
if orth_method is not None:
if s is None:
s = mol.intor_symmetric('cint1e_ovlp_sph')
corth = lo.orth.orth_ao(mol, method=orth_method, s=s)
cinv = numpy.dot(corth.T, s)
dm = reduce(numpy.dot, (cinv, dm, cinv.T))
else:
corth = numpy.eye(nao)
baslst = numpy.asarray(baslst)
notimp = numpy.asarray([i for i in range(nao) if i not in baslst])
occi, ui = scipy.linalg.eigh(-dm[baslst[:,None],baslst])
occi *= -1
idxi = numpy.argsort(abs(occi-1))
log.debug('entanglement weight occ = %s', str(occi[idxi]))
occb, ub = scipy.linalg.eigh(dm[notimp[:,None],notimp])
idxb = numpy.argsort(abs(occb-1))
log.debug('bath weight occ = %s', str(occb[idxb]))
if log.verbose >= logger.DEBUG:
log.debug('DMET %d impurity sites/occ', nimp)
label = mol.spheric_labels(True)
occ_label = ['#%d/%.5f'%(i+1,x) for i,x in enumerate(occi)]
dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,baslst], ui),
label=label, label2=occ_label, start=1)
nb = 0
for i in idxb:
if occ_cutoff < occb[i] < 2-occ_cutoff:
nb += 1
else:
break
log.debug('DMET %d entangled baths/occ', nb)
occ_label = ['#%d/%.5f'%(i+1,occb[j]) for i,j in enumerate(idxb)]
dump_mat.dump_rec(mol.stdout, numpy.dot(corth[:,notimp], ub[:,idxb[:nb]]),
label=label, label2=occ_label, start=1)
if baths is not None:
nbath = nao - nimp
mob = numpy.dot(corth[:,notimp], ub)
idxcas = idxb[baths]
idxenv = numpy.asarray([i for i in idxb if i not in idxcas])
idxenv = idxenv[numpy.argsort(-occb[idxenv])]
mo = numpy.hstack((mob[:,idxenv[:ncore]], numpy.dot(corth[:,baslst],ui),
mob[:,idxcas], mob[:,idxenv[ncore:]]))
occ = numpy.hstack((occb[idxenv[:ncore]], occi,
occb[idxcas], occb[idxenv[ncore:]]))
ncore_guess = (occb[idxenv[:ncore]]>2-occ_cutoff).sum()
nvirt_guess = (occb[idxenv[ncore:]]< occ_cutoff).sum()
elif 0: # The baths have largest occs
#occ = numpy.hstack((occi, occb))
idxb = numpy.argsort(occb)[::-1]
occ = numpy.hstack((occb[idxb[:ncore]], occi, occb[idxb[ncore:]]))
mob = numpy.dot(corth[:,notimp],ub[:,idxb])
mo = numpy.hstack((mob[:,:ncore], numpy.dot(corth[:,baslst],ui), mob[:,ncore:]))
ncore_guess = (occb>2-occ_cutoff).sum()
nvirt_guess = (occb<occ_cutoff).sum()
elif 1: # The baths have largest entanglement
mob = numpy.dot(corth[:,notimp], ub)
idxcas, idxenv = idxb[:ncas-nimp], idxb[ncas-nimp:]
idxenv = idxenv[numpy.argsort(-occb[idxenv])]
mo = numpy.hstack((mob[:,idxenv[:ncore]], numpy.dot(corth[:,baslst],ui),
mob[:,idxcas], mob[:,idxenv[ncore:]]))
occ = numpy.hstack((occb[idxenv[:ncore]], occi,
occb[idxcas], occb[idxenv[ncore:]]))
ncore_guess = (occb[idxenv[:ncore]]>2-occ_cutoff).sum()
nvirt_guess = (occb[idxenv[ncore:]]< occ_cutoff).sum()
else: # truncated impurity
occ = numpy.hstack((occi, occb))
occidx = numpy.argsort(occ)[::-1]
occ = occ[occidx]
mo = numpy.hstack((numpy.dot(corth[:,baslst],ui),
numpy.dot(corth[:,notimp],ub)))[:,occidx]
ncore_guess = (occ>2-occ_cutoff).sum()
nvirt_guess = (occ<occ_cutoff).sum()
casort = numpy.argsort(occ[ncore:nocc])[::-1] + ncore
#mo = numpy.hstack((mo[:,:ncore], mo[:,casort], mo[:,nocc:]))
#log.debug('active occs %s', occ[casort])
log.debug('active occs %s sum %s', occ[ncore:nocc], occ[ncore:nocc].sum())
if abs(2-occ[ncore-1]) > occ_cutoff:
log.info('Approx core space, core occ %g < 2', occ[ncore-1])
if abs(occ[nocc]) > occ_cutoff:
log.info('Truncate external space, occ %g > 0', occ[nocc])
ncas_guess = nao - ncore_guess - nvirt_guess
nelecas_guess = (ncore-ncore_guess+nelecas[0],
ncore-ncore_guess+nelecas[1])
return mo, ncas_guess, nelecas_guess, ncore_guess
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:
mf.dump_scf_summary(log)
nirrep = len(mol.irrep_id)
ovlp_ao = mf.get_ovlp()
orbsyma, orbsymb = mf.get_orbsym(mo_coeff, ovlp_ao)
orbsyma_in_d2h = numpy.asarray(orbsyma) % 10
orbsymb_in_d2h = numpy.asarray(orbsymb) % 10
tot_sym = 0
noccsa = [sum(orbsyma_in_d2h[mo_occ[0]>0]==ir) for ir in mol.irrep_id]
noccsb = [sum(orbsymb_in_d2h[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