def calc_localized_orbitals(mf,mol,method='ER',jmol=False):
# mf ... pyscf calculation object
# mol ... pyscf geometry object
# method ... localization method: ER, FB, PM
# jmol ... debug option to check furher 3d information files
# Localization.
# Spin 1.
# only occupied orbitals
mo_occ = mf.mo_coeff[0][:,mf.mo_occ[0]>0]
if method == 'ER':
loc1 = edmiston.Edmiston(mol, mo_occ)
if method == 'FB':
loc1 = boys.Boys(mol, mo_occ)
if method == 'PM':
loc1 = pipek.PipekMezey(mol, mo_occ)
orb1 = loc1.kernel()
# Spin 2
# only occupied orbitals
mo_occ = mf.mo_coeff[1][:,mf.mo_occ[1]>0]
if method == 'ER':
loc2 = edmiston.Edmiston(mol, mo_occ)
if method == 'FB':
loc2 = boys.Boys(mol, mo_occ)
if method == 'PM':
loc2 = pipek.PipekMezey(mol, mo_occ)
orb2 = loc2.kernel()
# Write orbitals for jmol format.
if jmol == True:
# Spin 1.
tools.molden.from_mo(mol, 'orb1.molden', orb1)
with open('orb1.spt', 'w') as f:
f.write('load orb1.molden; isoSurface MO 001;\n')
# Spin 2.
tools.molden.from_mo(mol, 'orb2.molden', orb2)
with open('orb2.spt', 'w') as f:
f.write('load orb2.molden; isoSurface MO 001;\n')
# Write orbitals in cube format.
# Spin 1.
occ = len(mf.mo_coeff[0][mf.mo_occ[0] == 1])
for i in range(occ):
orbital(mol, str(method)+'_orb_'+str(i)+'spin1.cube', orb1[:,i], nx=80, ny=80, nz=80)
# Spin 2.
occ = len(mf.mo_coeff[1][mf.mo_occ[1] == 1])
for i in range(occ):
orbital(mol, str(method)+'_orb_'+str(i)+'spin2.cube', orb2[:,i], nx=80, ny=80, nz=80)
def test_pipek(self):
idx = numpy.array([17,20,21,22,23,30,36,41,42,47,48,49])-1
loc = pipek.PipekMezey(mol)
mo = loc.kernel(mf.mo_coeff[:,idx])
pop = pipek.atomic_pops(mol, mo)
z = numpy.einsum('xii,xii->', pop, pop)
self.assertAlmostEqual(z, 12, 4)
def test_pipek_becke_scheme(self):
loc = pipek.PipekMezey(h2o, mf_h2o.mo_coeff[:, 3:8])
loc.pop_method = 'becke'
mo = loc.kernel()
pop = pipek.atomic_pops(h2o, mo)
z = numpy.einsum('xii,xii->', pop, pop)
self.assertAlmostEqual(z, 3.548139685217463, 4)
def test_pipek_exp4(self):
loc = pipek.PipekMezey(h2o, mf_h2o.mo_coeff[:, 3:8])
loc.exponent = 4
loc.max_cycle = 100
mo = loc.kernel()
pop = pipek.atomic_pops(h2o, mo)
z = numpy.einsum('xii,xii->', pop, pop)
self.assertAlmostEqual(z, 3.5368940222128247, 4)
def test_pipek(self):
idx = numpy.array([17, 20, 21, 22, 23, 30, 36, 41, 42, 47, 48, 49]) - 1
# Initial guess from Boys localization. Otherwise uncertainty between
# two solutions found in PM kernel
mo = boys.Boys(mol, mf.mo_coeff[:, idx]).kernel()
loc = pipek.PipekMezey(mol, mo)
loc.max_cycle = 100
mo = loc.kernel()
pop = pipek.atomic_pops(mol, mo)
z = numpy.einsum('xii,xii->', pop, pop)
self.assertAlmostEqual(z, 12, 4)
