def loc_orbs(mol: gto.Mole, mo_coeff: Tuple[np.ndarray, np.ndarray], \
s: np.ndarray, ref: str, variant: str) -> np.ndarray:
"""
this function returns a set of localized MOs of a specific variant
"""
# loop over spins
for i, spin_mo in enumerate((mol.alpha, mol.beta)):
if variant == 'fb':
# foster-boys procedure
loc = lo.Boys(mol, mo_coeff[i][:, spin_mo])
loc.conv_tol = LOC_CONV
# FB MOs
mo_coeff[i][:, spin_mo] = loc.kernel()
elif variant == 'pm':
# pipek-mezey procedure
loc = lo.PM(mol, mo_coeff[i][:, spin_mo])
loc.conv_tol = LOC_CONV
# PM MOs
mo_coeff[i][:, spin_mo] = loc.kernel()
elif 'ibo' in variant:
# orthogonalized IAOs
iao = lo.iao.iao(mol, mo_coeff[i][:, spin_mo])
iao = lo.vec_lowdin(iao, s)
# IBOs
mo_coeff[i][:, spin_mo] = lo.ibo.ibo(mol, mo_coeff[i][:, spin_mo], iaos=iao, \
grad_tol = LOC_CONV, exponent=int(variant[-1]), verbose=0)
# closed-shell reference
if ref == 'restricted' and mol.spin == 0:
mo_coeff[i + 1][:, spin_mo] = mo_coeff[i][:, spin_mo]
break
return mo_coeff
from pyscf import lo
from pyscf.tools import molden
mol = gto.M(
atom = '''
C 0.000000000000 1.398696930758 0.000000000000
C 0.000000000000 -1.398696930758 0.000000000000
C 1.211265339156 0.699329968382 0.000000000000
C 1.211265339156 -0.699329968382 0.000000000000
C -1.211265339156 0.699329968382 0.000000000000
C -1.211265339156 -0.699329968382 0.000000000000
H 0.000000000000 2.491406946734 0.000000000000
H 0.000000000000 -2.491406946734 0.000000000000
H 2.157597486829 1.245660462400 0.000000000000
H 2.157597486829 -1.245660462400 0.000000000000
H -2.157597486829 1.245660462400 0.000000000000
H -2.157597486829 -1.245660462400 0.000000000000''',
basis = '6-31g')
mf = scf.RHF(mol).run()
pz_idx = numpy.array([17,20,21,22,23,30,36,41,42,47,48,49])-1
loc_orb = lo.Boys(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'boys.molden', loc_orb)
loc_orb = lo.ER(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'edmiston.molden', loc_orb)
loc_orb = lo.PM(mol, mf.mo_coeff[:,pz_idx]).kernel()
molden.from_mo(mol, 'pm.molden', loc_orb)
#!/usr/bin/env python ''' PM localization for PBC systems. It supports gamma point only. ''' import numpy as np from pyscf.pbc import gto from pyscf.pbc import scf from pyscf import lo cell = gto.Cell() cell.atom = ''' C 3.17500000 3.17500000 3.17500000 H 2.54626556 2.54626556 2.54626556 H 3.80373444 3.80373444 2.54626556 H 2.54626556 3.80373444 3.80373444 H 3.80373444 2.54626556 3.80373444 ''' cell.basis = 'sto3g' cell.a = np.eye(3) * 6.35 cell.build() mf = scf.RHF(cell).density_fit().run() lmo = lo.PM(cell, mf.mo_coeff[:, 1:5]).kernel() nk = [1, 1, 1] abs_kpts = cell.make_kpts(nk) kmf = scf.KRHF(cell, abs_kpts).density_fit().run() lmo = lo.PM(cell, kmf.mo_coeff[0][:, 1:5]).kernel()
def init(self,molecule,charge,spin,basis_set,orb_basis='scf',cas=False,cas_nstart=None,cas_nstop=None,cas_nel=None,loc_nstart=None,loc_nstop=None,
scf_conv_tol=1e-14):
# {{{
import pyscf
from pyscf import gto, scf, ao2mo, molden, lo
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
#PYSCF inputs
print(" ---------------------------------------------------------")
print(" Using Pyscf:")
print(" ---------------------------------------------------------")
print(" ")
mol = gto.Mole()
mol.atom = molecule
mol.max_memory = 1000 # MB
mol.symmetry = True
mol.charge = charge
mol.spin = spin
mol.basis = basis_set
mol.build()
print("symmertry")
print(mol.topgroup)
#SCF
#mf = scf.RHF(mol).run(init_guess='atom')
mf = scf.RHF(mol).run(conv_tol=scf_conv_tol)
#C = mf.mo_coeff #MO coeffs
enu = mf.energy_nuc()
print(" SCF Total energy: %12.8f" %mf.e_tot)
print(" SCF Elec energy: %12.8f" %(mf.e_tot-enu))
print(mf.get_fock())
print(np.linalg.eig(mf.get_fock())[0])
if mol.symmetry == True:
from pyscf import symm
mo = symm.symmetrize_orb(mol, mf.mo_coeff)
osym = symm.label_orb_symm(mol, mol.irrep_name, mol.symm_orb, mo)
#symm.addons.symmetrize_space(mol, mo, s=None, check=True, tol=1e-07)
for i in range(len(osym)):
print("%4d %8s %16.8f"%(i+1,osym[i],mf.mo_energy[i]))
#orbitals and lectrons
n_orb = mol.nao_nr()
n_b , n_a = mol.nelec
nel = n_a + n_b
self.n_orb = mol.nao_nr()
if cas == True:
cas_norb = cas_nstop - cas_nstart
from pyscf import mcscf
assert(cas_nstart != None)
assert(cas_nstop != None)
assert(cas_nel != None)
else:
cas_nstart = 0
cas_nstop = n_orb
cas_nel = nel
##AO 2 MO Transformation: orb_basis or scf
if orb_basis == 'scf':
print("\nUsing Canonical Hartree Fock orbitals...\n")
C = cp.deepcopy(mf.mo_coeff)
print("C shape")
print(C.shape)
elif orb_basis == 'lowdin':
assert(cas == False)
S = mol.intor('int1e_ovlp_sph')
print("Using lowdin orthogonalized orbitals")
C = lowdin(S)
#end
elif orb_basis == 'boys':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :cas_nstart]
cl_a = lo.Boys(mol, mf.mo_coeff[:, cas_nstart:cas_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, cas_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'boys2':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :loc_nstart]
cl_a = lo.Boys(mol, mf.mo_coeff[:, loc_nstart:loc_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, loc_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'PM':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :cas_nstart]
cl_a = lo.PM(mol, mf.mo_coeff[:, cas_nstart:cas_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, cas_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'PM2':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :loc_nstart]
cl_a = lo.PM(mol, mf.mo_coeff[:, loc_nstart:loc_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, loc_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'ER':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :cas_nstart]
cl_a = lo.PM(mol, mf.mo_coeff[:, cas_nstart:cas_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, cas_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'ER2':
pyscf.lib.num_threads(1) #with degenerate states and multiple processors there can be issues
cl_c = mf.mo_coeff[:, :loc_nstart]
cl_a = lo.ER(mol, mf.mo_coeff[:, loc_nstart:loc_nstop]).kernel(verbose=4)
cl_v = mf.mo_coeff[:, loc_nstop:]
C = np.column_stack((cl_c, cl_a, cl_v))
elif orb_basis == 'ibmo':
loc_vstop = loc_nstop - n_a
print(loc_vstop)
mo_occ = mf.mo_coeff[:,mf.mo_occ>0]
mo_vir = mf.mo_coeff[:,mf.mo_occ==0]
c_core = mo_occ[:,:loc_nstart]
iao_occ = lo.iao.iao(mol, mo_occ[:,loc_nstart:])
iao_vir = lo.iao.iao(mol, mo_vir[:,:loc_vstop])
c_out = mo_vir[:,loc_vstop:]
# Orthogonalize IAO
iao_occ = lo.vec_lowdin(iao_occ, mf.get_ovlp())
iao_vir = lo.vec_lowdin(iao_vir, mf.get_ovlp())
#
# Method 1, using Knizia's alogrithm to localize IAO orbitals
#
'''
Generate IBOS from orthogonal IAOs
'''
ibo_occ = lo.ibo.ibo(mol, mo_occ[:,loc_nstart:], iaos = iao_occ)
ibo_vir = lo.ibo.ibo(mol, mo_vir[:,:loc_vstop], iaos = iao_vir)
C = np.column_stack((c_core,ibo_occ,ibo_vir,c_out))
else:
print("Error:NO orbital basis defined")
molden.from_mo(mol, 'orbitals.molden', C)
if cas == True:
print(C.shape)
print(cas_norb)
print(cas_nel)
mycas = mcscf.CASSCF(mf, cas_norb, cas_nel)
h1e_cas, ecore = mycas.get_h1eff(mo_coeff = C) #core core orbs to form ecore and eff
h2e_cas = ao2mo.kernel(mol, C[:,cas_nstart:cas_nstop], aosym='s4',compact=False).reshape(4 * ((cas_norb), ))
print(h1e_cas)
print(h1e_cas.shape)
#return h1e_cas,h2e_cas,ecore,C,mol,mf
self.h = h1e_cas
self.g = h2e_cas
self.ecore = ecore
self.mf = mf
self.mol = mol
self.C = cp.deepcopy(C[:,cas_nstart:cas_nstop])
J,K = mf.get_jk()
self.J = self.C.T @ J @ self.C
self.K = self.C.T @ J @ self.C
#HF density
if orb_basis == 'scf':
#C = C[:,cas_nstart:cas_nstop]
D = mf.make_rdm1(mo_coeff=C)
S = mf.get_ovlp()
sal, svec = np.linalg.eigh(S)
idx = sal.argsort()[::-1]
sal = sal[idx]
svec = svec[:, idx]
sal = sal**-0.5
sal = np.diagflat(sal)
X = svec @ sal @ svec.T
C_ao2mo = np.linalg.inv(X) @ C
Cocc = C_ao2mo[:, :n_a]
D = Cocc @ Cocc.T
DMO = C_ao2mo.T @ D @ C_ao2mo
#only for cas space
DMO = DMO[cas_nstart:cas_nstop,cas_nstart:cas_nstop]
self.dm_aa = DMO
self.dm_bb = DMO
print("DENSITY")
print(self.dm_aa.shape)
if 0:
h = C.T.dot(mf.get_hcore()).dot(C)
g = ao2mo.kernel(mol,C,aosym='s4',compact=False).reshape(4*((n_orb),))
const,heff = get_eff_for_casci(cas_nstart,cas_nstop,h,g)
print(heff)
print("const",const)
print("ecore",ecore)
idx = range(cas_nstart,cas_nstop)
h = h[:,idx]
h = h[idx,:]
g = g[:,:,:,idx]
g = g[:,:,idx,:]
g = g[:,idx,:,:]
g = g[idx,:,:,:]
self.ecore = const
self.h = h + heff
self.g = g
elif cas==False:
h = C.T.dot(mf.get_hcore()).dot(C)
g = ao2mo.kernel(mol,C,aosym='s4',compact=False).reshape(4*((n_orb),))
print(h)
#return h, g, enu, C,mol,mf
self.h = h
self.g = g
self.ecore = enu
self.mf = mf
self.mol = mol
self.C = C
J,K = mf.get_jk()
self.J = self.C.T @ J @ self.C
self.K = self.C.T @ J @ self.C
#HF density
if orb_basis == 'scf':
D = mf.make_rdm1(mo_coeff=None)
S = mf.get_ovlp()
sal, svec = np.linalg.eigh(S)
idx = sal.argsort()[::-1]
sal = sal[idx]
svec = svec[:, idx]
sal = sal**-0.5
sal = np.diagflat(sal)
X = svec @ sal @ svec.T
C_ao2mo = np.linalg.inv(X) @ C
Cocc = C_ao2mo[:, :n_a]
D = Cocc @ Cocc.T
DMO = C_ao2mo.T @ D @ C_ao2mo
self.dm_aa = DMO
self.dm_bb = DMO
print("DENSITY")
print(self.dm_aa)
def localize(pyscf_mf, loc_type='pm', verbose=0):
""" Localize orbitals given a PySCF mean-field object
Args:
pyscf_mf: PySCF mean field object
loc_type (str): localization type;
Pipek-Mezey ('pm') or Edmiston-Rudenberg ('er')
verbose (int): print level during localization
Returns:
pyscf_mf: Updated PySCF mean field object with localized orbitals
"""
# Note: After loading with `load_casfile_to_pyscf()` you can quiet message
# by resetting mf.mol, i.e., mf.mol = gto.M(...)
# but this assumes you have the *exact* molecular specification on hand.
# I've gotten acceptable results by restoring mf.mol this way (usually
# followed by calling mf.kernel()). But consistent localization is not a
# given (not unique) despite restoring data this way, hence the message.
if len(pyscf_mf.mol.atom) == 0:
sys.exit("`localize()` requires atom loc. and atomic basis to be" + \
" defined.\n " + \
"It also can be sensitive to the initial guess and MO" + \
" coefficients.\n " + \
"Best to try re-creating the PySCF molecule and doing the" + \
" SCF, rather than\n " + \
"try to load the mean-field object with" + \
" `load_casfile_to_pyscf()`. You can \n " + \
"try to provide the missing information, but consistency" + \
" cannot be guaranteed!")
# Split-localize (localize DOCC, SOCC, and virtual separately)
docc_idx = np.where(np.isclose(pyscf_mf.mo_occ, 2.))[0]
socc_idx = np.where(np.isclose(pyscf_mf.mo_occ, 1.))[0]
virt_idx = np.where(np.isclose(pyscf_mf.mo_occ, 0.))[0]
# Pipek-Mezey
if loc_type.lower() == 'pm':
print("Localizing doubly occupied ... ", end="")
loc_docc_mo = lo.PM(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, docc_idx]).kernel(verbose=verbose)
print("singly occupied ... ", end="")
loc_socc_mo = lo.PM(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, socc_idx]).kernel(verbose=verbose)
print("virtual ... ", end="")
loc_virt_mo = lo.PM(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, virt_idx]).kernel(verbose=verbose)
print("DONE")
# Edmiston-Rudenberg
elif loc_type.lower() == 'er':
print("Localizing doubly occupied ... ", end="")
loc_docc_mo = lo.ER(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, docc_idx]).kernel(verbose=verbose)
print("singly occupied ... ", end="")
loc_socc_mo = lo.ER(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, socc_idx]).kernel(verbose=verbose)
print("virtual ... ", end="")
loc_virt_mo = lo.ER(
pyscf_mf.mol,
pyscf_mf.mo_coeff[:, virt_idx]).kernel(verbose=verbose)
print("DONE")
# overwrite orbitals with localized orbitals
pyscf_mf.mo_coeff[:, docc_idx] = loc_docc_mo.copy()
pyscf_mf.mo_coeff[:, socc_idx] = loc_socc_mo.copy()
pyscf_mf.mo_coeff[:, virt_idx] = loc_virt_mo.copy()
return pyscf_mf
def init_pyscf(molecule, charge, spin, basis, orbitals):
# {{{
#PYSCF inputs
print(" ---------------------------------------------------------")
print(" ")
print(" Using Pyscf:")
print(" ")
print(" ---------------------------------------------------------")
print(" ")
mol = gto.Mole()
mol.atom = molecule
# this is needed to prevent openblas - openmp clash for some reason
# todo: take out
lib.num_threads(1)
mol.max_memory = 1000 # MB
mol.charge = charge
mol.spin = spin
mol.basis = basis
mol.build()
#orbitals and electrons
n_orb = mol.nao_nr()
n_b, n_a = mol.nelec
nel = n_a + n_b
#SCF
mf = scf.RHF(mol).run()
#mf = scf.ROHF(mol).run()
C = mf.mo_coeff #MO coeffs
S = mf.get_ovlp()
print(" Orbs1:")
print(C)
Cl = cp.deepcopy(C)
if orbitals == "boys":
print("\nUsing Boys localised orbitals:\n")
cl_o = lo.Boys(mol, mf.mo_coeff[:, :n_a]).kernel(verbose=4)
cl_v = lo.Boys(mol, mf.mo_coeff[:, n_a:]).kernel(verbose=4)
Cl = np.column_stack((cl_o, cl_v))
elif orbitals == "pipek":
print("\nUsing Pipek-Mezey localised orbitals:\n")
cl_o = lo.PM(mol, mf.mo_coeff[:, :n_a]).kernel(verbose=4)
cl_v = lo.PM(mol, mf.mo_coeff[:, n_a:]).kernel(verbose=4)
Cl = np.column_stack((cl_o, cl_v))
elif orbitals == "edmiston":
print("\nUsing Edmiston-Ruedenberg localised orbitals:\n")
cl_o = lo.ER(mol, mf.mo_coeff[:, :n_a]).kernel(verbose=4)
cl_v = lo.ER(mol, mf.mo_coeff[:, n_a:]).kernel(verbose=4)
Cl = np.column_stack((cl_o, cl_v))
# elif orbitals == "svd":
# print("\nUsing SVD localised orbitals:\n")
# cl_o = cp.deepcopy(mf.mo_coeff[:,:n_a])
# cl_v = cp.deepcopy(mf.mo_coeff[:,n_a:])
#
# [U,s,V] = np.linalg.svd(cl_o)
# cl_o = cl_o.dot(V.T)
# Cl = np.column_stack((cl_o,cl_v))
elif orbitals == "canonical":
print("\nUsing Canonical orbitals:\n")
pass
else:
print("Error: Wrong orbital specification:")
exit()
print(" Overlap:")
print(C.T.dot(S).dot(Cl))
# sort by cluster
blocks = [[0, 1, 2, 3], [4, 5, 6, 7]]
O = Cl[:, :n_a]
V = Cl[:, n_a:]
[sorted_order, cluster_sizes] = mulliken_clustering(blocks, mol, O)
O = O[:, sorted_order]
[sorted_order, cluster_sizes] = mulliken_clustering(blocks, mol, V)
V = V[:, sorted_order]
Cl = np.column_stack((O, V))
C = cp.deepcopy(Cl)
# dump orbitals for viewing
molden.from_mo(mol, 'orbitals_canon.molden', C)
molden.from_mo(mol, 'orbitals_local.molden', Cl)
##READING INTEGRALS FROM PYSCF
E_nu = gto.Mole.energy_nuc(mol)
T = mol.intor('int1e_kin_sph')
V = mol.intor('int1e_nuc_sph')
hcore = T + V
S = mol.intor('int1e_ovlp_sph')
g = mol.intor('int2e_sph')
print("\nSystem and Method:")
print(mol.atom)
print("Basis set :%12s" % (mol.basis))
print("Number of Orbitals :%10i" % (n_orb))
print("Number of electrons :%10i" % (nel))
print("Nuclear Repulsion :%16.10f " % E_nu)
print("Electronic SCF energy :%16.10f " %
(mf.e_tot - E_nu))
print("SCF Energy :%16.10f" %
(mf.e_tot))
print(" AO->MO")
g = np.einsum("pqrs,pl->lqrs", g, C)
g = np.einsum("lqrs,qm->lmrs", g, C)
g = np.einsum("lmrs,rn->lmns", g, C)
g = np.einsum("lmns,so->lmno", g, C)
h = reduce(np.dot, (C.conj().T, hcore, C))
# #mf = mf.density_fit(auxbasis='weigend')
# #mf._eri = None
# mcc = cc.UCCSD(mf)
# eris = mcc.ao2mo()
# eris.g = g
# eris.focka = h
# eris.fockb = h
#
# emp2, t1, t2 = mcc.init_amps(eris)
# exit()
# print(abs(t2).sum() - 4.9318753386922278)
# print(emp2 - -0.20401737899811551)
# t1, t2 = update_amps(mcc, t1, t2, eris)
# print(abs(t1).sum() - 0.046961325647584914)
# print(abs(t2).sum() - 5.378260578551683 )
#
#
# exit()
return (n_orb, n_a, n_b, h, g, mol, E_nu, mf.e_tot, C, S)
mol = gto.M(
atom=open('Ru_ph_ph_ph.xyz').read(),
unit='ang',
basis='STO3G',
charge=2,
verbose=3,
symmetry='C1',
max_memory=13000,
)
mf = mol.HF().run()
# split localizing by Pipek-Mezey
if len(sys.argv) == 2 and sys.argv[1] == 'localized':
print("Using PM localized orbitals")
C = np.hstack((lo.PM(mol, mf.mo_coeff[:, mf.mo_occ > 0]).kernel(),
lo.PM(mol, mf.mo_coeff[:, mf.mo_occ == 0]).kernel()))
else:
print("Using RHF orbitals")
C = mf.mo_coeff
tree = t3ns.T3NS(mol, c=C, network='T3NS')
tree.kernel(D=50, doci=True, max_sweeps=10, verbosity=2)
tree.disentangle()
tree.kernel(D=50, doci=True, max_sweeps=10, verbosity=2)
E = tree.kernel(D=100,
doci=True,
max_sweeps=100,
energy_conv=1e-5,
cell.pseudo = 'gth-pade'
cell.verbose = 5
cell.build(unit='Angstrom')
mf = scf.RHF(cell)
mf.kernel()
'''
generates IAOs
'''
mo_occ = mf.mo_coeff[:, mf.mo_occ > 0]
#a = lo.iao.iao(cell, mo_occ, minao='minao')
#a = lo.iao.iao(cell, mo_occ, minao='gth-szv')
a = iao.iao(cell, mo_occ, minao='gth-szv', scf_basis=True,
ref_basis='gth-szv') # scf basis
print "IAO shape: ", a.shape
molden.from_mo(cell, 'diamondiao_szv.molden', a)
# Orthogonalize IAO
a = lo.vec_lowdin(a, mf.get_ovlp())
molden.from_mo(cell, 'diamondiao_szv_ortho.molden', a)
loc_obj = lo.PM(cell, a)
cost_before = loc_obj.cost_function()
print "cost function before localization: ", cost_before
loc_orb = loc_obj.kernel()
molden.from_mo(cell, 'diamondiao_szv_PM.molden', loc_orb)
#ibo must take the orthonormalized IAOs
#ibo = lo.ibo.ibo(cell, mo_occ, a)
#print "IBO shape: ", ibo.shape
#molden.from_mo(cell, 'diamondibo_szv_ibo.molden', ibo)
mycas = mcscf.CASSCF(mf, 6, 6)
# Be careful with the keyword argument "base". By default sort_mo function takes
# the 1-based indices. The return indices of .argsort() method above are 0-based
cas_orbs = mycas.sort_mo(cas_list, mf.mo_coeff, base=0)
mycas.kernel(cas_orbs)
#
# Localized orbitals are often used as the initial guess of CASSCF method.
# When localizing SCF orbitals, it's better to call the localization twice to
# obtain the localized orbitals for occupied space and virtual space
# separately. This split localization scheme can ensure that the initial core
# determinant sits inside the HF occupied space.
#
nocc = mol.nelectron // 2
loc1 = lo.PM(mol, mf.mo_coeff[:, :nocc]).kernel()
loc2 = lo.PM(mol, mf.mo_coeff[:, nocc:]).kernel()
loc_orbs = numpy.hstack((loc1, loc2))
pz_pop = mo_mapping.mo_comps('C 2pz', mol, loc_orbs)
cas_list = pz_pop.argsort()[-6:]
print('cas_list', cas_list)
print('pz population for active space orbitals', pz_pop[cas_list])
#
# Symmetry was enabled in this molecule. By default, symmetry-adapted CASSCF
# algorithm will be called for molecule with symmetry. However, the orbital
# localization above breaks the orbital spatial symmetry. If proceeding the
# symmetry-adapted CASSCF calculation, the program may complain that the
# CASSCF initial guess is not symmetrized after certain attempts of orbital
# symmetrization. The simplest operation for this problem is to mute the
# spatial symmetry of the molecule.
