H = HubbardHamiltonian(H_mol, U=3.5)
H.read_density('mol-ref/density.nc')
H.iterate(density.calc_n_insulator)
p = plot.Charge(H, ext_geom=molecule, colorbar=True)
p.savefig('chg.pdf')
p = plot.ChargeDifference(H, ext_geom=molecule, colorbar=True)
p.savefig('chgdiff.pdf')
p = plot.SpinPolarization(H, ext_geom=molecule, colorbar=True, vmax=0.2)
p.annotate()
p.savefig('pol.pdf')
H.H.shift(-H.find_midgap())
ev, evec = H.eigh(eigvals_only=False, spin=0)
p = plot.Wavefunction(H, 500 * evec[:, 10], ext_geom=molecule, colorbar=True)
p.savefig('wf.pdf')
p = plot.Spectrum(H)
p.savefig('spectrum.pdf')
p = plot.DOSmap(H)
p.savefig('2Ddos_map.pdf')
p = plot.PDOS(H, np.linspace(-0.2, 0.2, 101))
p.savefig('total_dos.pdf')
p = plot.PDOS(H, np.linspace(-0.2, 0.2, 101), sites=[60])
dn = H.converge(density.calc_n, tol=1e-10, steps=10, mixer=mixer)
Etot0 = H.Etot
n = 1 * H.n
# Obtain DOS for the finite molecule with Lorentzian distribution
egrid = np.linspace(-1, 1, 50)
import hubbard.plot as plot
H.H.shift(-H.fermi_level())
p = plot.DOS(H, egrid, eta=1e-2, spin=0)
# Now compute same molecule with the WBL approximation with gamma=0
from hubbard.negf import NEGF
elec = sisl.WideBandSE(2, 0.)
negf = NEGF(H, [elec], [[0, 1]])
# This is to use a better guess for the device potential
negf.Ef = H.find_midgap()
negf.eta = 1e-2
mixer.clear()
dn = H.converge(negf.calc_n_open,
mixer=mixer,
tol=1e-10,
func_args={'qtol': 1e-4},
steps=1,
print_info=True)
print('Total energy difference: %.4e eV' % (Etot0 - H.Etot))
print('Density difference (up, dn): (%.4e, %.4e)' %
(max(abs(H.n[0] - n[0])), max(abs(H.n[1] - n[1]))))
# Plot DOS calculated from the diagonalization and the WBL with gamma=0
H.H.shift(-negf.Ef)
dos = negf.DOS(H, egrid, spin=0)
import sisl
# Build sisl Geometry object
mol = sisl.get_sile('type1.xyz').read_geometry()
mol.sc.set_nsc([1, 1, 1])
mol = mol.move(-mol.center(what='xyz')).rotate(220, [0, 0, 1])
# 3NN tight-binding model
Hsp2 = sp2(mol, t1=2.7, t2=0.2, t3=.18)
H = HubbardHamiltonian(Hsp2)
# Plot the single-particle TB (U = 0.0) wavefunction (SO) for Type 1
H.U = 0.0
ev, evec = H.eigh(eigvals_only=False, spin=0)
N = H.q[0]
midgap = H.find_midgap()
ev -= midgap
f = 3800
v = evec[:, int(round(N)) - 1]
j = np.argmax(abs(v))
wf = f * v**2 * np.sign(v[j]) * np.sign(v)
p = plot.Wavefunction(H, wf)
p.set_title(r'$E = %.3f$ eV' % (ev[int(round(N)) - 1]))
p.savefig('Fig3_SOMO.pdf')
# Plot MFH spin polarization for U = 3.5 eV
H.U = 3.5
success = H.read_density(
'fig3_type1.nc') # Try reading, if we already have density on file
if not success:
H.set_polarization([23])
molecule = sisl.get_sile('mol-ref/mol-ref.XV').read_geometry()
molecule.sc.set_nsc([1, 1, 1])
Hsp2 = sp2(molecule)
H = HubbardHamiltonian(Hsp2, U=2.0)
H.set_polarization([36], [77])
dn = H.converge(density.calc_n_insulator,
mixer=sisl.mixing.LinearMixer(),
tol=1e-7)
print('Closed-shell spin-polarized calculation:')
print('dn: {}, Etot: {}\n'.format(dn, H.Etot))
p = plot.Plot()
for i in range(2):
ev = H.eigh(spin=i) - H.find_midgap()
ev = ev[abs(ev) < 2]
p.axes.plot(ev,
np.zeros_like(ev), ['or', 'xg'][i],
label=[r'$\sigma=\uparrow$', r'$\sigma=\downarrow$'][i])
# Compute same system with spin degeneracy
Hsp2 = sp2(molecule, spin='unpolarized')
H = HubbardHamiltonian(Hsp2, U=2.0)
dn = H.converge(density.calc_n_insulator,
mixer=sisl.mixing.LinearMixer(),
tol=1e-7)
print('Unpolarized calculation:')
print('dn: {}, Etot: {}'.format(dn, H.Etot))
ev = H.eigh() - H.find_midgap()