# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom vector_c = [0.0, 0.0, 7.06373620597]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates left_electrode_coordinates = [[ 0.72107876, 1.24846289, 1.17728937], [ 3.60483699, 1.24846289, 1.17728937], [ 6.48859522, 1.24846289, 1.17728937], [-0.72080035, 3.74587078, 1.17728937], [ 5.04671611, 3.74587078, 1.17728937], [ 2.16295788, 3.74587078, 1.17728937], [ 3.60483699, 6.24327867, 1.17728937], [-2.16267947, 6.24327867, 1.17728937], [ 0.72107876, 6.24327867, 1.17728937], [ 2.16295788, 2.08093219, 3.5318681 ], [-0.72080035, 2.08093219, 3.5318681 ], [ 5.04671611, 2.08093219, 3.5318681 ], [-3.60455858, 7.07574796, 3.5318681 ], [-2.16267947, 4.57834008, 3.5318681 ], [ 2.16295788, 7.07574796, 3.5318681 ], [ 3.60483699, 4.57834008, 3.5318681 ], [ 0.72107876, 4.57834008, 3.5318681 ], [-0.72080035, 7.07574796, 3.5318681 ], [ 7.93047434, 0.4159936 , 5.88644684], [ 0.72107876, 2.91340148, 5.88644684], [ 2.16295788, 5.41080937, 5.88644684], [-0.72080035, 5.41080937, 5.88644684], [ 5.04671611, 5.41080937, 5.88644684], [ 2.16295788, 0.4159936 , 5.88644684], [ 3.60483699, 2.91340148, 5.88644684], [ 5.04671611, 0.4159936 , 5.88644684], [ 6.48859522, 2.91340148, 5.88644684]]*Angstrom # Set up configuration left_electrode = BulkConfiguration( bravais_lattice=left_electrode_lattice, elements=left_electrode_elements, cartesian_coordinates=left_electrode_coordinates ) # ------------------------------------------------------------- # Right Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom vector_c = [0.0, 0.0, 7.06373620597]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates right_electrode_coordinates = [[ 0.72080035, 4.57882217, 1.17728937], [-0.72107876, 7.07623006, 1.17728937], [ 2.16267947, 7.07623006, 1.17728937], [-2.16295788, 4.57882217, 1.17728937], [-0.72107876, 2.08141429, 1.17728937], [ 3.60455858, 4.57882217, 1.17728937], [-3.60483699, 7.07623006, 1.17728937], [ 5.0464377 , 2.08141429, 1.17728937], [ 2.16267947, 2.08141429, 1.17728937], [ 7.93019593, 0.4164757 , 3.5318681 ], [ 3.60455858, 2.91388358, 3.5318681 ], [ 6.48831681, 2.91388358, 3.5318681 ], [ 2.16267947, 5.41129147, 3.5318681 ], [ 5.0464377 , 0.4164757 , 3.5318681 ], [ 5.0464377 , 5.41129147, 3.5318681 ], [-0.72107876, 5.41129147, 3.5318681 ], [ 0.72080035, 2.91388358, 3.5318681 ], [ 2.16267947, 0.4164757 , 3.5318681 ], [ 2.16267947, 3.74635288, 5.88644684], [-2.16295788, 6.24376076, 5.88644684], [ 0.72080035, 6.24376076, 5.88644684], [-0.72107876, 3.74635288, 5.88644684], [ 6.48831681, 1.24894499, 5.88644684], [ 0.72080035, 1.24894499, 5.88644684], [ 5.0464377 , 3.74635288, 5.88644684], [ 3.60455858, 1.24894499, 5.88644684], [ 3.60455858, 6.24376076, 5.88644684]]*Angstrom # Set up configuration right_electrode = BulkConfiguration( bravais_lattice=right_electrode_lattice, elements=right_electrode_elements, cartesian_coordinates=right_electrode_coordinates ) # ------------------------------------------------------------- # Central Region # ------------------------------------------------------------- # Set up lattice vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom vector_c = [0.0, 0.0, 21.4923367139]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Sulfur, Carbon, Hydrogen, Hydrogen, Carbon, Carbon, Carbon, Carbon, Hydrogen, Hydrogen, Carbon, Sulfur, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates central_region_coordinates = [[ 0.72107876, 1.24846289, 1.17728937], [ 3.60483699, 1.24846289, 1.17728937], [ 6.48859522, 1.24846289, 1.17728937], [ -0.72080035, 3.74587078, 1.17728937], [ 5.04671611, 3.74587078, 1.17728937], [ 2.16295788, 3.74587078, 1.17728937], [ 3.60483699, 6.24327867, 1.17728937], [ -2.16267947, 6.24327867, 1.17728937], [ 0.72107876, 6.24327867, 1.17728937], [ 2.16295788, 2.08093219, 3.5318681 ], [ -0.72080035, 2.08093219, 3.5318681 ], [ 5.04671611, 2.08093219, 3.5318681 ], [ -3.60455858, 7.07574796, 3.5318681 ], [ -2.16267947, 4.57834008, 3.5318681 ], [ 2.16295788, 7.07574796, 3.5318681 ], [ 3.60483699, 4.57834008, 3.5318681 ], [ 0.72107876, 4.57834008, 3.5318681 ], [ -0.72080035, 7.07574796, 3.5318681 ], [ 7.93047434, 0.4159936 , 5.88644684], [ 0.72107876, 2.91340148, 5.88644684], [ 2.16295788, 5.41080937, 5.88644684], [ -0.72080035, 5.41080937, 5.88644684], [ 5.04671611, 5.41080937, 5.88644684], [ 2.16295788, 0.4159936 , 5.88644684], [ 3.60483699, 2.91340148, 5.88644684], [ 5.04671611, 0.4159936 , 5.88644684], [ 6.48859522, 2.91340148, 5.88644684], [ 2.16295788, 3.74587078, 7.59644684], [ 2.16295788, 3.74587078, 9.34644649], [ 1.07984884, 5.62136998, 9.49557904], [ 3.24594854, 1.87057656, 9.49607409], [ 1.55660877, 4.79581794, 10.04613074], [ 2.76904869, 2.69637089, 10.04634658], [ 1.55658866, 4.79585277, 11.44599014], [ 2.76902857, 2.69640571, 11.44620598], [ 1.0796888 , 5.6216471 , 11.99626262], [ 3.24578851, 1.87085367, 11.99675768], [ 2.16267947, 3.74635288, 12.14589023], [ 2.16267947, 3.74635288, 13.89588988], [ 0.72080035, 4.57882217, 15.60588988], [ -0.72107876, 7.07623006, 15.60588988], [ 2.16267947, 7.07623006, 15.60588988], [ -2.16295788, 4.57882217, 15.60588988], [ -0.72107876, 2.08141429, 15.60588988], [ 3.60455858, 4.57882217, 15.60588988], [ -3.60483699, 7.07623006, 15.60588988], [ 5.0464377 , 2.08141429, 15.60588988], [ 2.16267947, 2.08141429, 15.60588988], [ 7.93019593, 0.4164757 , 17.96046861], [ 3.60455858, 2.91388358, 17.96046861], [ 6.48831681, 2.91388358, 17.96046861], [ 2.16267947, 5.41129147, 17.96046861], [ 5.0464377 , 0.4164757 , 17.96046861], [ 5.0464377 , 5.41129147, 17.96046861], [ -0.72107876, 5.41129147, 17.96046861], [ 0.72080035, 2.91388358, 17.96046861], [ 2.16267947, 0.4164757 , 17.96046861], [ 2.16267947, 3.74635288, 20.31504735], [ -2.16295788, 6.24376076, 20.31504735], [ 0.72080035, 6.24376076, 20.31504735], [ -0.72107876, 3.74635288, 20.31504735], [ 6.48831681, 1.24894499, 20.31504735], [ 0.72080035, 1.24894499, 20.31504735], [ 5.0464377 , 3.74635288, 20.31504735], [ 3.60455858, 1.24894499, 20.31504735], [ 3.60455858, 6.24376076, 20.31504735]]*Angstrom # Set up configuration central_region = BulkConfiguration( bravais_lattice=central_region_lattice, elements=central_region_elements, cartesian_coordinates=central_region_coordinates ) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode] ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = [ CerdaHuckelParameters.Gold_fcc_Basis, HoffmannHuckelParameters.Carbon_Basis, HoffmannHuckelParameters.Hydrogen_Basis, HoffmannHuckelParameters.Sulfur_Basis, ] #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( shift_to_gamma=(False, False, False), na=3, nb=3, nc=100, ) left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=left_electrode_k_point_sampling, ) right_electrode_k_point_sampling = MonkhorstPackGrid( shift_to_gamma=(False, False, False), na=3, nb=3, nc=100, ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=right_electrode_k_point_sampling, ) device_k_point_sampling = MonkhorstPackGrid( shift_to_gamma=(False, False, False), na=3, nb=3, nc=100, ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=device_k_point_sampling, ) #---------------------------------------- # Iteration Control Settings #---------------------------------------- left_electrode_iteration_control_parameters = IterationControlParameters() right_electrode_iteration_control_parameters = IterationControlParameters() device_iteration_control_parameters = IterationControlParameters() #---------------------------------------- # Poisson Solver Settings #---------------------------------------- left_electrode_poisson_solver = FastFourier2DSolver( boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()], [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()], [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]] ) right_electrode_poisson_solver = FastFourier2DSolver( boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()], [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()], [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]] ) #---------------------------------------- # Device Algorithm Settings #---------------------------------------- initial_density_type = EquivalentBulk( electrode_constraint_length=10.0*Angstrom, ) device_algorithm_parameters = DeviceAlgorithmParameters( initial_density_type=initial_density_type, ) #---------------------------------------- # Electrode Calculators #---------------------------------------- left_electrode_calculator = HuckelCalculator( basis_set=basis_set, numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters, iteration_control_parameters=left_electrode_iteration_control_parameters, poisson_solver=left_electrode_poisson_solver, ) right_electrode_calculator = HuckelCalculator( basis_set=basis_set, numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters, iteration_control_parameters=right_electrode_iteration_control_parameters, poisson_solver=right_electrode_poisson_solver, ) #---------------------------------------- # Device Calculator #---------------------------------------- calculator = DeviceHuckelCalculator( basis_set=basis_set, numerical_accuracy_parameters=device_numerical_accuracy_parameters, iteration_control_parameters=device_iteration_control_parameters, device_algorithm_parameters=device_algorithm_parameters, electrode_calculators= [left_electrode_calculator, right_electrode_calculator], ) device_configuration.setCalculator(calculator) nlprint(device_configuration) device_configuration.update() nlsave('au_dtb_au.nc', device_configuration) # ------------------------------------------------------------- # Transmission Spectrum # ------------------------------------------------------------- kpoint_grid = MonkhorstPackGrid( shift_to_gamma=(False, False, False), na=1, nb=1, nc=1, ) transmission_spectrum = TransmissionSpectrum( configuration=device_configuration, energies=numpy.linspace(-1,1,51)*eV, kpoints=kpoint_grid, energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=KrylovSelfEnergy(), ) nlsave('au_dtb_au.nc', transmission_spectrum) nlprint(transmission_spectrum)