ASF = asf.asf()
mol = gto.Mole()
mol.atom = """
C 0.00000 0.00000 0.00000
C 0.00000 0.00000 1.20000
"""
mol.basis = 'def2-svp'
mol.charge = 0
mol.spin = 0
mol.build()
# UHF for UNOs
mf = scf.RHF(mol).run(max_cycle=100)
mo_new = mf.stability()[0]
while mo_new is not mf.mo_coeff:
mf.kernel(dm0=mf.make_rdm1(mo_coeff=mo_new))
mo_new = mf.stability()[0]
# AVAS initial guess.
ao_labels = ['C 2s', 'C 2p']
norb, ne_act, orbs = avas.avas(mf, ao_labels, canonicalize=False)
# Plot AVAS selected orbitals.
# orbital list
fao = asf.act_fao(mf.mo_occ, ne_act)
orblist = fao + np.array(list(range(norb)))
asf.visualize_mos(mol, orbs, orblist)
# Select an active space using entropies.
ele, mos = ASF.find_active_space(mol, ne_act, norb, orbs, plot=True)
# core: 1s2 2s2 2p6 3s2 3p6 (18e, 9o)
# active: 3d10 4s1/ 3d9 4s2 (11e, 11o)
ao_lb = gto.sph_labels(mol)
for i in range(30):
ivs = np.argsort(mf.mo_coeff[:, i]**2)
ss = ""
for iv in ivs[::-1][:3]:
ss += "%10.6f (%s)" % (mf.mo_coeff[iv, i]**2, ao_lb[iv].strip())
print(" MO %2d :: %s" % (i, ss))
print("\n CASSCF(12, 11):\n")
from pyscf.mcscf import avas
ao_labels = ['Cu 3d', 'Cu 4s']
norb, ne_act, orbs = avas.avas(mf,
ao_labels,
threshold=0.001,
canonicalize=True)
print(norb, ne_act)
mc = mcscf.CASSCF(mf, norb, ne_act)
mc.state_average_((0.5, 0.1, 0.1, 0.1, 0.1, 0.1))
mc.kernel(orbs)
# cas_list = [9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26]
# mc = mcscf.CASSCF(mf, 11, (6, 5))
# mc.fix_spin_(ss=0.75)
# mo = mcscf.sort_mo(mc, mf.mo_coeff, cas_list, base=0)
# mc.state_average_((0.5, 0.1, 0.1, 0.1, 0.1, 0.1))
# mc.kernel(mo)
print(mc.nelecas, mc.e_states)
def avas_active_space(pyscf_mf,
ao_list=None,
molden_fname='avas_localized_orbitals',
**kwargs):
""" Return AVAS active space as PySCF molecule and mean-field object
Args:
pyscf_mf: PySCF mean field object
Kwargs:
ao_list: list of strings of AOs (print mol.ao_labels() to see options)
Example: ao_list = ['H 1s', 'O 2p', 'O 2s'] for water
verbose (bool): do additional print
molden_fname (str): MOLDEN filename to save AVAS active space orbitals.
Default is to save
to 'avas_localized_orbitals.molden'
**kwargs: other keyworded arguments to pass into avas.avas()
Returns:
pyscf_active_space_mol: Updated PySCF molecule object from
AVAS-selected active space
pyscf_active_space_mf: Updated PySCF mean field object from
AVAS-selected active space
"""
# Note: requires openshell_option = 3 for this to work, which keeps all
# singly occupied in CAS
# we also require canonicalize = False so that we don't destroy local orbs
avas_output = avas.avas(pyscf_mf,
ao_list,
canonicalize=False,
openshell_option=3,
**kwargs)
active_norb, active_ne, reordered_orbitals = avas_output
active_alpha, _ = get_num_active_alpha_beta(pyscf_mf, active_ne)
if molden_fname is not None:
# save set of localized orbitals for active space
if isinstance(pyscf_mf, scf.rohf.ROHF):
frozen_alpha = pyscf_mf.nelec[0] - active_alpha
assert frozen_alpha >= 0
else:
frozen_alpha = pyscf_mf.mol.nelectron // 2 - active_alpha
assert frozen_alpha >= 0
active_space_idx = slice(frozen_alpha, frozen_alpha + active_norb)
active_mos = reordered_orbitals[:, active_space_idx]
tools.molden.from_mo(pyscf_mf.mol,
molden_fname + '.molden',
mo_coeff=active_mos)
# Choosing an active space changes the molecule ("freezing" electrons,
# for example), so we
# form the active space tensors first, then re-form the PySCF objects to
# ensure consistency
pyscf_active_space_mol, pyscf_active_space_mf = cas_to_pyscf(
*pyscf_to_cas(pyscf_mf,
cas_orbitals=active_norb,
cas_electrons=active_ne,
avas_orbs=reordered_orbitals))
return pyscf_active_space_mol, pyscf_active_space_mf
''' mol.basis = 'cc-pvtz-dk' mol.spin = 0 mol.build() mf = scf.ROHF(mol).x2c() mf.kernel() # # The active space can be generated by pyscf.mcscf.avas.avas function # from pyscf.mcscf import avas # See also 43-dmet_cas.py and function gto.mole.search_ao_label for the rules # of "ao_labels" in the following ao_labels = ['Fe 3d', 'C 2pz'] norb, ne_act, orbs = avas.avas(mf, ao_labels, canonicalize=False) weights = numpy.ones(13)/13 solver1 = fci.addons.fix_spin(fci.direct_spin1.FCI(mol), ss=2) # <S^2> = 2 for Triplet solver1.spin = 2 solver1.nroots = 6 solver2 = fci.addons.fix_spin(fci.direct_spin1.FCI(mol), ss=0) # <S^2> = 0 for Singlet solver2.spin = 0 solver2.nroots = 7 mycas = mcscf.CASSCF(mf, norb, ne_act) mycas.chkfile ='fecp2_3dpz.chk' mcscf.state_average_mix_(mycas, [solver1, solver2], weights) mycas.verbose = 6 mycas.kernel(orbs)
Cl 1.639807 -1.639807 -0.539657
Cl -1.639807 -1.639807 -0.539657
''',
basis = 'cc-pvtz-dk',
spin = 1,
charge = -2,
verbose = 5)
mf = scf.sfx2c1e(scf.ROHF(mol))
mf.chkfile = 'vocl4.chk'
mf.kernel()
#
# Generate the DMRG-CASSCF initial guess with AVAS (atomic valence active space) method.
#
norb_act, ne_act, mos = avas.avas(mf, ['V 3s', 'V 3p', 'V 3d', 'O 2p', 'Cl 3p'])
#
# Pass 1
# DMRG-CASSCF calculation with small M. In many systems, the mcscf orbitals has
# weak dependence to the quality of the active space solution. We can use small
# M to approximate the active space wave function and increase M for DMRG-CASCI
# and DMRG-NEVPT2 in next step.
#
mc = dmrgscf.DMRGSCF(mf, norb_act, ne_act)
mc.fcisolver.maxM = 500
mc.fcisolver.extraline = ['num_thrds %d'%lib.num_threads(), 'warmup local_2site']
mc.fcisolver.memory = 100 # GB
mc.conv_tol = 1e-6
mc.state_average_([.2]*3)
mc.kernel(mos)
H 0.000000 2.292835 1.638208
H 2.180615 0.708525 1.638208
H 1.347694 -1.854942 1.638208
'''
mol.basis = 'cc-pvtz-dk'
mol.spin = 0
mol.build()
mf = scf.sfx2c1e(scf.ROHF(mol))
mf.kernel()
#
# The active space can be generated by pyscf.mcscf.avas.avas function
#
from pyscf.mcscf import avas
norb, ne_act, orbs = avas.avas(mf, ['Fe 3d', 'C 2pz'], canonicalize=False)
#
# The followings are the step-by-step solution to construct the active space
# based on the formulas provided by the paper.
#
#====================================================================
# To choose AOs for a given atom and a given shell to project into
#====================================================================
def AOset(mol, AO_id, l, shell):
AOs =[]
m=-l
for i in range (2*l+1):
AOs.append(mol.search_ao_nr(AO_id,l,m,shell))
m +=1
cell.precision = 1e-6 cell.a = ''' 0.000000000, 3.370137329, 3.370137329 3.370137329, 0.000000000, 3.370137329 3.370137329, 3.370137329, 0.000000000''' cell.unit = 'B' cell.verbose = 4 cell.build() mf = scf.RHF(cell).density_fit(auxbasis='def2-svp-jkfit') mf.exxdiv = None ehf = mf.kernel() from pyscf.mcscf import avas ao_labels = ['C 2s', 'C 2p'] norb, ne_act, orbs = avas.avas(mf, ao_labels, canonicalize=True, ncore=2) mc = mcscf.CASSCF(mf, norb, ne_act) #mc.fcisolver = fci.selected_ci_spin0.SCI() #mc.fix_spin_(shift=.5, ss=0.0000) #mc.fcisolver.ci_coeff_cutoff = 0.005 #mc.fcisolver.select_cutoff = 0.005 mc.kernel(orbs) nmo = mc.ncore + mc.ncas rdm1, rdm2 = mc.fcisolver.make_rdm12(mc.ci, mc.ncas, mc.nelecas) rdm1, rdm2 = mcscf.addons._make_rdm12_on_mo(rdm1, rdm2, mc.ncore, mc.ncas, nmo) #natocc, natorb = numpy.linalg.eigh(-rdm1) #for i, k in enumerate(numpy.argmax(abs(natorb), axis=0)): # if natorb[k,i] < 0:
H 0.000000 2.292835 1.638208
H 2.180615 0.708525 1.638208
H 1.347694 -1.854942 1.638208
'''
mol.basis = 'cc-pvtz-dk'
mol.spin = 0
mol.build()
mf = scf.sfx2c1e(scf.ROHF(mol))
mf.kernel()
#
# The active space can be generated by pyscf.mcscf.avas.avas function
#
from pyscf.mcscf import avas
norb, ne_act, orbs = avas.avas(mf, ['Fe 3d', 'C 2pz'], canonicalize=False)
#
# The followings are the step-by-step solution to construct the active space
# based on the formulas provided by the paper.
#
#====================================================================
# To choose AOs for a given atom and a given shell to project into
#====================================================================
def AOset(mol, AO_id, l, shell):
AOs = []
m = -l
for i in range(2 * l + 1):
AOs.append(mol.search_ao_nr(AO_id, l, m, shell))
