def init_guess_by_atom(mol):
'''Generate initial guess density matrix from superposition of atomic HF
density matrix. The atomic HF is occupancy averaged RHF
Returns:
Density matrix, 2D ndarray
'''
import copy
from pyscf.scf import atom_hf
from pyscf.scf import addons
atm_scf = atom_hf.get_atm_nrhf(mol)
mo = []
mo_occ = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb != 'GHOST':
if symb in atm_scf:
e_hf, e, c, occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, e, c, occ = atm_scf[symb]
mo.append(c)
mo_occ.append(occ)
mo = scipy.linalg.block_diag(*mo)
mo_occ = numpy.hstack(mo_occ)
pmol = copy.copy(mol)
pmol.cart = False
c = addons.project_mo_nr2nr(pmol, mo, mol)
dm = numpy.dot(c * mo_occ, c.T)
for k, v in atm_scf.items():
logger.debug1(mol, 'Atom %s, E = %.12g', k, v[0])
return dm
def init_guess_by_atom(mol):
'''Generate initial guess density matrix from superposition of atomic HF
density matrix. The atomic HF is occupancy averaged RHF
Returns:
Density matrix, 2D ndarray
'''
from pyscf.scf import atom_hf
atm_scf = atom_hf.get_atm_nrhf(mol)
nbf = mol.nao_nr()
dm = numpy.zeros((nbf, nbf))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in atm_scf:
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
p1 = p0 + mo_e.__len__()
dm[p0:p1,p0:p1] = numpy.dot(mo_c*mo_occ, mo_c.T.conj())
p0 = p1
for k, v in atm_scf.items():
logger.debug1(mol, 'Atom %s, E = %.12g', k, v[0])
return dm
def init_guess_by_atom(mol):
'''Generate initial guess density matrix from superposition of atomic HF
density matrix. The atomic HF is occupancy averaged RHF
Returns:
Density matrix, 2D ndarray
'''
from pyscf.scf import atom_hf
atm_scf = atom_hf.get_atm_nrhf(mol)
nbf = mol.nao_nr()
dm = numpy.zeros((nbf, nbf))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in atm_scf:
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
p1 = p0 + mo_e.__len__()
dm[p0:p1,p0:p1] = numpy.dot(mo_c*mo_occ, mo_c.T.conj())
p0 = p1
for k, v in atm_scf.items():
logger.debug1(mol, 'Atom %s, E = %.12g', k, v[0])
return dm
def get_dm(self): #, cycle=1):
'''
Get DM in configuration-adapted basis
steps:
1) Guess density matrix from superposition
of atomic HF density matrix
2) build Fock matrix
3) update DM by diagonalizing corresponding
Fock matrix
4) construct new DM
Note that the initial atomic DM was obtained through solving
the occupancy averaged RHF
Returns:
Density matrix, 2D ndarray
'''
mol = self.mol
atm_scf = atom_hf.get_atm_nrhf(mol)
aoslice = mol.aoslice_by_atom()
atm_dms = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in atm_scf:
symb = mol.atom_pure_symbol(ia)
if symb in atm_scf:
e_hf, e, c, occ = atm_scf[symb]
dm = np.dot(c * occ, c.conj().T)
else: # symb's basis is not specified in the input
nao_atm = aoslice[ia, 3] - aoslice[ia, 2]
dm = np.zeros((nao_atm, nao_atm))
atm_dms.append(dm)
dm = scipy.linalg.block_diag(*atm_dms)
if mol.cart:
cart2sph = mol.cart2sph_coeff(normalized='sp')
dm = reduce(np.dot, (cart2sph, dm, cart2sph.T))
mf = self.mf
#if cycle > 0:
vhf = mf.get_veff(mol, dm)
fock = mf.get_fock(self.h1e, self.s, vhf, dm)
mo_energy, mo_coeff = mf.eig(fock, self.s)
mo_occ = mf.get_occ(mo_energy, mo_coeff)
dm = mf.make_rdm1(mo_coeff, mo_occ)
return dm
def test_atom_hf_with_ecp(self):
mol = gto.M(verbose=7,
output='/dev/null',
atom='Cu 0 0 0; Ba 0 0 2',
basis={
'Ba': 'def2-svp',
'Cu': 'lanl2dz'
},
ecp={
'Ba': 'def2-svp',
'Cu': 'lanl2dz'
},
spin=None)
scf_result = atom_hf.get_atm_nrhf(mol)
self.assertAlmostEqual(scf_result['Ba'][0], -25.07089468572715, 9)
self.assertAlmostEqual(scf_result['Cu'][0], -194.92388639203045, 9)
def pre_orth_ao_atm_scf(mol):
from pyscf.scf import atom_hf
atm_scf = atom_hf.get_atm_nrhf(mol)
nbf = mol.nao_nr()
c = numpy.zeros((nbf, nbf))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in atm_scf:
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
p1 = p0 + mo_e.size
c[p0:p1,p0:p1] = mo_c
p0 = p1
return c
def pre_orth_ao_atm_scf(mol):
from pyscf.scf import atom_hf
atm_scf = atom_hf.get_atm_nrhf(mol)
nbf = mol.nao_nr()
c = numpy.zeros((nbf, nbf))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in atm_scf:
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, mo_e, mo_c, mo_occ = atm_scf[symb]
p1 = p0 + mo_e.size
c[p0:p1, p0:p1] = mo_c
p0 = p1
return c
def pre_orth_ao_atm_scf(mol):
assert (not mol.cart)
from pyscf.scf import atom_hf
atm_scf = atom_hf.get_atm_nrhf(mol)
aoslice = mol.aoslice_by_atom()
coeff = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in atm_scf:
symb = mol.atom_pure_symbol(ia)
if symb in atm_scf:
e_hf, e, c, occ = atm_scf[symb]
else: # symb's basis is not specified in the input
nao_atm = aoslice[ia, 3] - aoslice[ia, 2]
c = numpy.zeros((nao_atm, nao_atm))
coeff.append(c)
return scipy.linalg.block_diag(*coeff)
