def generate_skf(self, opt_val):
""" Generates all *-*.skf files for a given set of
confinement parameters
opt_val: the (internally defined) list of parameter values used
in setting up the confinement potentials (and hence
changing the Slater-Koster integrals).
"""
# Update the confinement parameters:
for i, (key, param) in enumerate(self.opt_param):
self.vconf[key].__setattr__(param, opt_val[i])
if self.verbose:
print('VCONF:')
for key in sorted(self.vconf):
print(' ' + key + ' : ' + str(self.vconf[key]))
# Run the atomic DFT calculations
for atom in self.atoms:
conf, wf_conf = None, {}
for key, vconf in self.vconf.items():
if '%s_n' % atom.symbol in key:
conf = vconf
else:
for nl in atom.valence:
if '%s_%s' % (atom.symbol, nl) in key:
wf_conf[nl] = vconf
if conf is not None:
atom.set_confinement(conf)
if wf_conf:
atom.set_wf_confinement(wf_conf)
atom.run()
# Perform the Slater-Koster integrations
for i, atom1 in enumerate(self.atoms):
s1 = atom1.symbol
for j in range(i + 1):
atom2 = self.atoms[j]
s2 = atom2.symbol
prefix1 = s1 + '-' + s2
prefix2 = s2 + '-' + s1
sk_kwargs = {}
for key, val in self.sk_kwargs.items():
if isinstance(val, dict):
if prefix1 in val:
sk_kwargs[key] = val[prefix1]
elif prefix2 in val:
sk_kwargs[key] = val[prefix2]
else:
sk_kwargs[key] = val['default']
else:
sk_kwargs[key] = val
sk = SlaterKosterTable(atom1, atom2, timing=False, txt=None)
sk.run(**sk_kwargs)
filename = '%s-%s.skf' % (s1, s2)
if s1 == s2:
sk.write(filename=filename, pair=(s1, s2), **atom1.info)
else:
sk.write(filename=filename, pair=(s1, s2))
filename = '%s-%s.skf' % (s2, s1)
sk.write(filename=filename, pair=(s2, s1))
return
default='potential',
help='Which superposition scheme? '
'Choose "potential" (default) or "density"')
p.add_option('-t', '--stride', default=1, type=int,
help='Which SK-table stride length? Default = 1. '
'See hotcent.slako.run for more information.')
opt, args = p.parse_args()
# Get KS all-electron ground state of confined atom:
element = 'C'
r0 = 1.85 * covalent_radii[atomic_numbers[element]] / Bohr
atom = AtomicDFT(element,
xc=opt.functional,
confinement=PowerConfinement(r0=r0, s=2),
configuration='[He] 2s2 2p2',
valence=['2s', '2p'],
timing=True,
)
atom.run()
atom.plot_Rnl(only_valence=False)
atom.plot_density()
# Compute Slater-Koster integrals:
rmin, dr, N = 0.5, 0.05, 250
sk = SlaterKosterTable(atom, atom, timing=True)
sk.run(rmin, dr, N, superposition=opt.superposition,
xc=opt.functional, stride=opt.stride)
sk.write('%s-%s_no_repulsion.par' % (element, element))
sk.write('%s-%s_no_repulsion.skf' % (element, element))
sk.plot()
U = atom.get_hubbard_value('2p', scheme='central', maxstep=1.)
hubbardvalues = {'s': U}
# -------------------------------
# Compute Slater-Koster integrals
# -------------------------------
r_cov = covalent_radii[atomic_numbers[element]] / Bohr
r_wfc = 2 * r_cov
r_rho = 3 * r_cov
atom = AtomicDFT(
element,
xc=xc,
confinement=PowerConfinement(r0=r_wfc, s=2),
wf_confinement=PowerConfinement(r0=r_rho, s=2),
configuration=configuration,
valence=valence,
scalarrel=False,
)
atom.run()
# Compute Slater-Koster integrals:
rmin, dr, N = 0.5, 0.05, 250
sk = SlaterKosterTable(atom, atom)
sk.run(rmin, dr, N, superposition='density', xc=xc)
sk.write('%s-%s_no_repulsion.skf' % (element, element),
eigenvalues=eigenvalues,
spe=0.,
hubbardvalues=hubbardvalues,
occupations=occupations)
scalarrel=True,
maxiter=50000,
mix=0.005,
txt='-',
)
atom.run()
atoms[el] = atom
# -------------------------------
# Compute Slater-Koster integrals
# -------------------------------
for i in range(len(elements)):
el_a = elements[i]
rNum = rNum2 / 2.0 if el == element2 else rNum1 / 2.0
for j in range(i + 1):
rNum = rNum + rNum2 / 2.0 if el == element2 else rNum + rNum1 / 2.0
el_b = elements[j]
rmin, dr, N = 0.4, 0.02, int(rNum)
sk = SlaterKosterTable(atoms[el_a], atoms[el_b], txt='-')
sk.run(rmin, dr, N, superposition='density', xc=xc, stride=2)
if el_a == el_b:
sk.write('%s-%s_no_repulsion.skf' % (el_a, el_a),
eigenvalues=eigenvalues[el_a],
spe=0.,
hubbardvalues=hubbardvalues[el_a],
occupations=occupations[el_a])
else:
for pair in [(el_a, el_b), (el_b, el_a)]:
sk.write('%s-%s_no_repulsion.skf' % pair, pair=pair)
conf = PowerConfinement(r0=9.41, s=2)
wf_conf = {
'5d': PowerConfinement(r0=6.50, s=2),
'6s': PowerConfinement(r0=6.50, s=2),
'6p': PowerConfinement(r0=4.51, s=2),
}
atom = AtomicDFT(
element,
xc=xc,
confinement=conf,
wf_confinement=wf_conf,
configuration='[Xe] 4f14 5d10 6s1 6p0',
valence=['5d', '6s', '6p'],
scalarrel=True,
timing=True,
nodegpts=150,
mix=0.2,
txt='-',
)
atom.run()
atom.plot_Rnl()
atom.plot_density()
# Compute Slater-Koster integrals:
rmin, dr, N = 0.4, 0.02, 900
sk = SlaterKosterTable(atom, atom, timing=True)
sk.run(rmin, dr, N, superposition='density', xc=xc)
sk.write('Au-Au_no_repulsion.par')
sk.write('Au-Au_no_repulsion.skf')
sk.plot()
atom2 = AtomicDFT(
'H',
xc='LDA',
confinement=PowerConfinement(r0=1.1, s=2),
configuration='1s1',
valence=['1s'],
txt=None,
)
atom2.run()
ener = atom2.get_energy()
print('H -- Etot | %s' % check(ener, 0.58885808402033557, eps_etot))
e_1s = atom2.get_epsilon('1s')
print('H -- E_1s | %s' % check(e_1s, 1.00949638195278960, eps))
# Check B-H Slater-Koster integrals
sk = SlaterKosterTable(atom1, atom2, txt=None)
R, nt, nr = 2.0, 150, 50
sk.wf_range = sk.get_range(1e-7)
grid, areas = sk.make_grid(R, nt=nt, nr=nr)
S, H, H2 = sk.calculate_mels([('sss', '2s', '1s')], atom1, atom2, R, grid,
areas)
print('B-H sps S | %s' % check_abs(S[9], -0.34627316, eps))
print('B-H sps H | %s' % check_abs(H[9], 0.29069894, eps))
print('B-H sps H2 | %s' % check_abs(H2[9], 0.29077536, eps))
S, H, H2 = sk.calculate_mels([('sps', '1s', '2p')], atom2, atom1, R, grid,
areas)