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])
p.savefig('pdos_energy_resolved.pdf')
p = plot.LDOS_from_eigenstate(H, evec[:, 10] * 200, sites=[60], ext_geom=molecule)
p.savefig('pdos.pdf')
# Test real-space plots?
from hubbard import HubbardHamiltonian, plot, sp2
import sys
import numpy as np
import sisl
# Build sisl Geometry object
mol = sisl.get_sile('junction-2-2.XV').read_geometry()
mol.sc.set_nsc([1, 1, 1])
mol = mol.move(-mol.center(what='xyz')).rotate(220, [0, 0, 1])
Hsp2 = sp2(mol)
# 3NN tight-binding model
H = HubbardHamiltonian(Hsp2, U=0)
# Plot Eigenspectrum
p = plot.Spectrum(H, ymax=0.12)
p.set_title(r'3NN, $U=%.2f$ eV' % H.U)
p.savefig('eigenspectrum_U%i.pdf' % (H.U * 100))
# Plot H**O and LUMO level wavefunctions for up- and down-electrons for U=3.5 eV
spin = ['up', 'dn']
N = H.q
for i in range(1):
ev, evec = H.eigh(eigvals_only=False, spin=i)
# Use midgap as energy reference
midgap = H.find_midgap()
ev -= midgap
f = 1
v = evec[:, int(round(N[i])) - 1]
j = np.argmax(abs(v))
wf = f * v**2 * np.sign(v[j]) * np.sign(v)