Skip to content

Instantly share code, notes, and snippets.

Embed
What would you like to do?
""" Bond disorder
Lattice : Honeycomb 1[nm] interatomic distance and t=1[eV] hopping;
Disorder : StructuralDisorder class bond and vacancy disorder;
Configuration : size of the system 512x512, without domain decomposition (nx=ny=1), periodic boundary conditions,
double precision, manual scaling;
Calculation : dos;
Modification : magnetic field is off;
"""
import numpy as np
import pybinding as pb
import kite
def honeycomb_lattice(onsite=(0, 0)):
"""Make a honeycomb lattice with nearest neighbor hopping"""
theta = np.pi / 3
a1 = np.array([1 + np.cos(theta), np.sin(theta)])
a2 = np.array([0, 2 * np.sin(theta)])
# create a lattice with 2 primitive vectors
lat = pb.Lattice(
a1=a1,
a2=a2
)
# Add sublattices
lat.add_sublattices(
# name, position, and onsite potential
('A', [0, 0], onsite[0]),
('B', [1, 0], onsite[1])
)
# Add hoppings
lat.add_hoppings(
# inside the main cell, between which atoms, and the value
([0, 0], 'A', 'B', - 1),
# between neighboring cells, between which atoms, and the value
([-1, 0], 'A', 'B', - 1),
([-1, 1], 'A', 'B', - 1),
)
# Add bond disorder as an object of a class StructuralDisorder. In this manner we can add onsite and bond defects
# with a specific concentration, which will be added to the simulated system. The procedure for adding is same
# as adding the hopping, with the difference that the bond disorded is not bounded to one site in the [0, 0]
# unit cell.
node0 = [[+0, +0], 'A']
node1 = [[+0, +0], 'B']
node2 = [[+1, +0], 'A']
node3 = [[+0, +1], 'B']
node4 = [[+0, +1], 'A']
node5 = [[-1, +1], 'B']
struc_disorder_one = kite.StructuralDisorder(lat, concentration=0.05)
struc_disorder_one.add_structural_disorder(
# add bond disorder in the form [from unit cell], 'sublattice_from', [to_unit_cell], 'sublattice_to', value:
(*node0, *node1, 1),
(*node1, *node2, 1),
(*node2, *node3, 1),
(*node3, *node4, 1),
(*node4, *node5, 1),
(*node5, *node0, 1),
# in this way we can add onsite disorder in the form [unit cell], 'sublattice', value
([+0, +0], 'B', 0.3)
)
# It is possible to add multiple different disorder type which should be forwarded to the export_lattice function
# as a list.
struc_disorder_two = kite.StructuralDisorder(lat, concentration=0.2)
struc_disorder_two.add_structural_disorder(
(*node0, *node1, 0.4),
(*node4, *node5, 0.4),
(*node5, *node0, 0.4),
([+0, +0], 'B', 0.4)
)
struc_disorder_two.add_vacancy('B')
struc_disorder_three = kite.StructuralDisorder(lat, concentration=0.01)
struc_disorder_three.add_vacancy('A')
# if there is disorder it should be returned separately from the lattice
return lat, [struc_disorder_one, struc_disorder_two, struc_disorder_three]
# load a honeycomb lattice and structural_disorder
lattice, disorder_structural = honeycomb_lattice()
# number of decomposition parts in each direction of matrix.
# This divides the lattice into various sections, each of which is calculated in parallel
nx = ny = 1
# number of unit cells in each direction.
lx = ly = 512
# make config object which caries info about
# - the number of decomposition parts [nx, ny],
# - lengths of structure [lx, ly]
# - boundary conditions, setting True as periodic boundary conditions, and False elsewise,
# - info if the exported hopping and onsite data should be complex,
# - info of the precision of the exported hopping and onsite data, 0 - float, 1 - double, and 2 - long double.
# - scaling, if None it's automatic, if present select spectrum_bound=[e_min, e_max]
configuration = kite.Configuration(divisions=[nx, ny], length=[lx, ly], boundaries=[True, True],
is_complex=False, precision=1, spectrum_range=[-15, 15])
# require the calculation of DOS
calculation = kite.Calculation(configuration)
calculation.dos(num_moments=1024, num_random=1, num_disorder=1, num_points=1000)
# configure the *.h5 file
kite.config_system(lattice, configuration, calculation, filename='structural_disorder.h5',
disorder_structural=disorder_structural)
@quantum-kite

This comment has been minimized.

Copy link
Owner Author

@quantum-kite quantum-kite commented Jun 5, 2018

image

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment