from hubbard import HubbardHamiltonian, sp2, ncsile
import sisl
import numpy as np
# Build sisl Geometry object only for a subset of atoms
molecule = sisl.get_sile('mol-ref/mol-ref.XV').read_geometry().sub([2,3,5])
molecule.sc.set_nsc([1, 1, 1])
# Build HubbardHamiltonian object
Hsp2 = sp2(molecule)
H = HubbardHamiltonian(Hsp2, U=3.5)
# Generate simple density
H.n = np.ones((2, H.sites))*0.5
print(f'1. Write and read densities under group {H.get_hash()} using the HubbardHamiltonian class\n')
# Write density in file
H.write_density('mol-ref/test.HU.nc', group=H.get_hash(), mode='w')
# Read density using the HubbardHamiltonian class
H.read_density('mol-ref/test.HU.nc', group=H.get_hash())
# Write another density in file under another group
print(f'2. Write another densities under another group\n')
H.n *= 2
H.write_density('mol-ref/test.HU.nc', group='group2', mode='a')
print('3. Read density, U and kT using ncsile from all groups')
fh = sisl.get_sile('mol-ref/test.HU.nc', mode='r')
for g in fh.groups:
print('group: ', g)
print('n:', fh.read_density(group=g))
n_AFM = H.n
f = open('FM-AFM.dat', 'w')
mixer = sisl.mixing.PulayMixer(0.7, history=7)
for u in np.arange(5, 0, -0.25):
# We approach the solutions for different U values
H.U = u
mixer.clear()
# AFM case first
success = H.read_density(
'clar-goblet.nc') # Try reading, if we already have density on file
if not success:
H.n = n_AFM.copy()
dn = H.converge(density.calc_n_insulator, tol=1e-10, mixer=mixer)
eAFM = H.Etot
H.write_density('clar-goblet.nc')
n_AFM = H.n.copy()
if u == 3.5:
p = plot.SpinPolarization(H, colorbar=True, vmax=0.4, vmin=-0.4)
p.savefig('spin_pol_U%i_AFM.pdf' % (H.U * 1000))
# Now FM case
H.q[0] += 1 # change to two more up-electrons than down
H.q[1] -= 1
success = H.read_density(
'clar-goblet.nc') # Try reading, if we already have density on file
# Map electrodes in the device region
elec_indx = [range(len(H_elec)), range(len(HC.H) - len(H_elec), len(HC.H))]
# MFH object of the device
MFH_HC = HubbardHamiltonian(HC.H, U=U, kT=kT)
# Initial densities
success = MFH_HC.read_density('HC_density.nc')
if not success:
# Get initial spin-densities with PBC to speed up the following convergence with OBC
n = MFH_elec.tile(16, axis=0).n
a = np.delete(n[0],
[67, 68, 69, 72, 73, 74, 77, 78, 79, 82, 83, 84, 87, 88, 89])
b = np.delete(n[1],
[67, 68, 69, 72, 73, 74, 77, 78, 79, 82, 83, 84, 87, 88, 89])
n = np.array([a, b])
MFH_HC.n = n
# First create NEGF object
negf = NEGF(MFH_HC, [(MFH_elec, '-A'), (MFH_elec, '+A')], elec_indx, V=0.1)
mixer.clear()
dn = MFH_HC.converge(negf.calc_n_open,
steps=1,
tol=1e-5,
mixer=mixer,
func_args={'qtol': 1e-4},
print_info=True)
print('Nup, Ndn: ', MFH_HC.n.sum(axis=1))
# Write also densities for future calculations
MFH_HC.write_density('HC_density.nc')
# Plot spin polarization of electrodes