from hubbard import HubbardHamiltonian, sp2, density, NEGF
import sisl
# Build sisl Geometry object
molecule = sisl.get_sile('mol-ref/mol-ref.XV').read_geometry()
molecule.sc.set_nsc([1, 1, 1])
print('1. Run one iteration with calc_n_insulator')
Hsp2 = sp2(molecule)
H = HubbardHamiltonian(Hsp2, U=3.5)
H.random_density()
dn = H.iterate(density.calc_n_insulator, mixer=sisl.mixing.LinearMixer())
print(' dn, Etot: ', dn, H.Etot, '\n')
print('2. Run one iteration with data from ncfile')
H.read_density('mol-ref/density.nc', group='3abe772')
dn = H.iterate(density.calc_n_insulator, mixer=sisl.mixing.LinearMixer())
etot = 1 * H.Etot
print(' dn, Etot: ', dn, etot, '\n')
print('3. Run one iteration with calc_n')
d = H.iterate(density.calc_n, mixer=sisl.mixing.LinearMixer())
e = H.Etot
print(' dn, dEtot: ', d - dn, e - etot, '\n')
# Write fdf-block
print('\n4. Write initspin to fdf-block')
H.write_initspin('test.fdf', mode='w')
import random
print('5. Run one iteration for spin-degenerate calculation')
# Test all plot functionalities of hubbard module
# 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])
molecule = molecule.move(-molecule.center(what='xyz')).rotate(220, [0, 0, 1])
H_mol = sp2(molecule)
p = plot.BondHoppings(H_mol, annotate=False, off_diagonal_only=False, cmap_e='winter')
p.legend()
p.savefig('bondHoppings.pdf')
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)
from hubbard import HubbardHamiltonian, sp2, density
import sisl
# Build sisl Geometry object
molecule = sisl.get_sile('mol-ref/mol-ref.XV').read_geometry()
molecule.sc.set_nsc([1, 1, 1])
print('1. Run one iteration with calc_n_insulator')
Hsp2 = sp2(molecule)
H = HubbardHamiltonian(Hsp2, U=3.5)
H.random_density()
dn = H.iterate(density.calc_n_insulator, mixer=sisl.mixing.LinearMixer())
print(' dn, Etot: ', dn, H.Etot, '\n')
print('2. Run one iteration with data from ncfile')
H.read_density('mol-ref/density.nc')
dn = H.iterate(density.calc_n_insulator, mixer=sisl.mixing.LinearMixer())
etot = 1 * H.Etot
print(' dn, Etot: ', dn, etot, '\n')
print('3. Run one iteration with calc_n')
d = H.iterate(density.calc_n, mixer=sisl.mixing.LinearMixer())
e = H.Etot
print(' dn, dEtot: ', d - dn, e - etot, '\n')
# Write new data structure
print('4. Write data in ncfile')
H.write_density('mol-ref/test.nc', mode='w')
# Write fdf-block
print('\n5. Write initspin to fdf-block')