# Test quantitatively that densities and eigenvalue spectrum are unchanged
# using a reference molecule (already converged)
# Build sisl Geometry object
molecule = sisl.get_sile('mol-ref/mol-ref.XV').read_geometry()
molecule.sc.set_nsc([1, 1, 1])
# Try reading from file
Hsp2 = sp2(molecule)
H = HubbardHamiltonian(Hsp2, U=3.5)
H.read_density('mol-ref/density.nc')
H.iterate(density.calc_n_insulator, mixer=sisl.mixing.LinearMixer())
# Determine reference values for the tests
ev0, evec0 = H.eigh(eigvals_only=False, spin=0)
Etot0 = 1 * H.Etot
mixer = sisl.mixing.PulayMixer(0.7, history=7)
for m in [density.calc_n_insulator, density.calc_n]:
# Reset density and iterate
H.random_density()
mixer.clear()
dn = H.converge(m, tol=1e-10, steps=10, mixer=mixer, print_info=True)
ev1, evec1 = H.eigh(eigvals_only=False, spin=0)
# Total energy check:
print('Total energy difference: %.4e eV' % (Etot0 - H.Etot))
# Eigenvalues are easy to check
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])
p.savefig('pdos_energy_resolved.pdf')
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()