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# quantum-kite/structural_disorder.py

Last active Jun 10, 2018
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 """ 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 commented Jun 5, 2018

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