# ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [8.65127, 0.0, 0.0]*Angstrom vector_b = [-4.32564, 7.49222, 0.0]*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. , 0. , 1.177246838306], [ 2.883758230374, 0. , 1.177246838306], [ 5.767516460748, 0. , 1.177246838306], [-1.441879115187, 2.497407885876, 1.177246838306], [ 1.441879115187, 2.497407885876, 1.177246838306], [ 4.325637345561, 2.497407885876, 1.177246838306], [-2.883758230374, 4.994815771753, 1.177246838306], [-0. , 4.994815771753, 1.177246838306], [ 2.883758230374, 4.994815771753, 1.177246838306], [ 1.441879115187, 0.832469295292, 3.531825573629], [ 4.325637345561, 0.832469295292, 3.531825573629], [ 7.209395575935, 0.832469295292, 3.531825573629], [-0. , 3.329877181169, 3.531825573629], [ 2.883758230374, 3.329877181169, 3.531825573629], [ 5.767516460748, 3.329877181169, 3.531825573629], [-1.441879115187, 5.827285067045, 3.531825573629], [ 1.441879115187, 5.827285067045, 3.531825573629], [ 4.325637345561, 5.827285067045, 3.531825573629], [-0. , 1.664938590584, 5.886404308952], [ 2.883758230374, 1.664938590584, 5.886404308952], [ 5.767516460748, 1.664938590584, 5.886404308952], [-1.441879115187, 4.162346476461, 5.886404308952], [ 1.441879115187, 4.162346476461, 5.886404308952], [ 4.325637345561, 4.162346476461, 5.886404308952], [-2.883758230374, 6.659754362337, 5.886404308952], [-0. , 6.659754362337, 5.886404308952], [ 2.883758230374, 6.659754362337, 5.886404308952]]*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 = [8.65127, 0.0, 0.0]*Angstrom vector_b = [-4.32564, 7.49222, 0.0]*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. , 1.664938590584, 1.177331897016], [ 2.883758230374, 1.664938590584, 1.177331897016], [ 5.767516460748, 1.664938590584, 1.177331897016], [-1.441879115187, 4.162346476461, 1.177331897016], [ 1.441879115187, 4.162346476461, 1.177331897016], [ 4.325637345561, 4.162346476461, 1.177331897016], [-2.883758230374, 6.659754362337, 1.177331897016], [-0. , 6.659754362337, 1.177331897016], [ 2.883758230374, 6.659754362337, 1.177331897016], [ 1.441879115187, 0.832469295292, 3.531910632339], [ 4.325637345561, 0.832469295292, 3.531910632339], [ 7.209395575935, 0.832469295292, 3.531910632339], [-0. , 3.329877181169, 3.531910632339], [ 2.883758230374, 3.329877181169, 3.531910632339], [ 5.767516460748, 3.329877181169, 3.531910632339], [-1.441879115187, 5.827285067045, 3.531910632339], [ 1.441879115187, 5.827285067045, 3.531910632339], [ 4.325637345561, 5.827285067045, 3.531910632339], [ 0. , 0. , 5.886489367661], [ 2.883758230374, 0. , 5.886489367661], [ 5.767516460748, 0. , 5.886489367661], [-1.441879115187, 2.497407885876, 5.886489367661], [ 1.441879115187, 2.497407885876, 5.886489367661], [ 4.325637345561, 2.497407885876, 5.886489367661], [-2.883758230374, 4.994815771753, 5.886489367661], [-0. , 4.994815771753, 5.886489367661], [ 2.883758230374, 4.994815771753, 5.886489367661]]*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 = [8.65127, 0.0, 0.0]*Angstrom vector_b = [-4.32564, 7.49222, 0.0]*Angstrom vector_c = [0.0, 0.0, 26.1842542284]*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, 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, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates central_region_coordinates = [[ 0. , 0. , 1.177246838306], [ 2.883758230374, 0. , 1.177246838306], [ 5.767516460748, 0. , 1.177246838306], [ -1.441879115187, 2.497407885876, 1.177246838306], [ 1.441879115187, 2.497407885876, 1.177246838306], [ 4.325637345561, 2.497407885876, 1.177246838306], [ -2.883758230374, 4.994815771753, 1.177246838306], [ -0. , 4.994815771753, 1.177246838306], [ 2.883758230374, 4.994815771753, 1.177246838306], [ 1.441879115187, 0.832469295292, 3.531825573629], [ 4.325637345561, 0.832469295292, 3.531825573629], [ 7.209395575935, 0.832469295292, 3.531825573629], [ -0. , 3.329877181169, 3.531825573629], [ 2.883758230374, 3.329877181169, 3.531825573629], [ 5.767516460748, 3.329877181169, 3.531825573629], [ -1.441879115187, 5.827285067045, 3.531825573629], [ 1.441879115187, 5.827285067045, 3.531825573629], [ 4.325637345561, 5.827285067045, 3.531825573629], [ -0. , 1.664938590584, 5.886404308952], [ 2.883758230374, 1.664938590584, 5.886404308952], [ 5.767516460748, 1.664938590584, 5.886404308952], [ -1.441879115187, 4.162346476461, 5.886404308952], [ 1.441879115187, 4.162346476461, 5.886404308952], [ 4.325637345561, 4.162346476461, 5.886404308952], [ -2.883758230374, 6.659754362337, 5.886404308952], [ -0. , 6.659754362337, 5.886404308952], [ 2.883758230374, 6.659754362337, 5.886404308952], [ 0. , 0. , 8.240983044274], [ 2.883758230374, 0. , 8.240983044274], [ 5.767516460748, 0. , 8.240983044274], [ -1.441879115187, 2.497407885876, 8.240983044274], [ 1.441879115187, 2.497407885876, 8.240983044274], [ 4.325637345561, 2.497407885876, 8.240983044274], [ -2.883758230374, 4.994815771753, 8.240983044274], [ -0. , 4.994815771753, 8.240983044274], [ 2.883758230374, 4.994815771753, 8.240983044274], [ -0. , 3.329877181169, 9.950983044274], [ 0.000167598274, 3.330000988149, 11.700983031869], [ 2.141113495536, 3.104457648599, 11.849212743505], [ -2.140744100558, 3.555570150149, 11.849240681067], [ 1.19830836185 , 3.203799621127, 12.396521536067], [ -1.19793542389 , 3.456256114907, 12.39656493323 ], [ 1.198435435614, 3.203780838187, 13.787656477468], [ -1.197806007547, 3.456195085679, 13.787696164708], [ 2.141237198973, 3.10441690481 , 14.335054536015], [ -2.140622838979, 3.555422091299, 14.335071137123], [ 0.000320116744, 3.329990265468, 14.483271217051], [ -0. , 3.329877181169, 16.233271184118], [ 0. , 0. , 17.943271184118], [ 2.883758230374, 0. , 17.943271184118], [ 5.767516460748, 0. , 17.943271184118], [ -1.441879115187, 2.497407885876, 17.943271184118], [ 1.441879115187, 2.497407885876, 17.943271184118], [ 4.325637345561, 2.497407885876, 17.943271184118], [ -2.883758230374, 4.994815771753, 17.943271184118], [ -0. , 4.994815771753, 17.943271184118], [ 2.883758230374, 4.994815771753, 17.943271184118], [ 0. , 1.664938590584, 20.297849919441], [ 2.883758230374, 1.664938590584, 20.297849919441], [ 5.767516460748, 1.664938590584, 20.297849919441], [ -1.441879115187, 4.162346476461, 20.297849919441], [ 1.441879115187, 4.162346476461, 20.297849919441], [ 4.325637345561, 4.162346476461, 20.297849919441], [ -2.883758230374, 6.659754362337, 20.297849919441], [ -0. , 6.659754362337, 20.297849919441], [ 2.883758230374, 6.659754362337, 20.297849919441], [ 1.441879115187, 0.832469295292, 22.652428654764], [ 4.325637345561, 0.832469295292, 22.652428654764], [ 7.209395575935, 0.832469295292, 22.652428654764], [ -0. , 3.329877181169, 22.652428654764], [ 2.883758230374, 3.329877181169, 22.652428654764], [ 5.767516460748, 3.329877181169, 22.652428654764], [ -1.441879115187, 5.827285067045, 22.652428654764], [ 1.441879115187, 5.827285067045, 22.652428654764], [ 4.325637345561, 5.827285067045, 22.652428654764], [ 0. , 0. , 25.007007390086], [ 2.883758230374, 0. , 25.007007390086], [ 5.767516460748, 0. , 25.007007390086], [ -1.441879115187, 2.497407885876, 25.007007390086], [ 1.441879115187, 2.497407885876, 25.007007390086], [ 4.325637345561, 2.497407885876, 25.007007390086], [ -2.883758230374, 4.994815771753, 25.007007390086], [ -0. , 4.994815771753, 25.007007390086], [ 2.883758230374, 4.994815771753, 25.007007390086]]*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 = [ LDABasis.Hydrogen_DoubleZetaPolarized, LDABasis.Carbon_DoubleZetaPolarized, LDABasis.Sulfur_DoubleZetaPolarized, LDABasis.Gold_SingleZetaPolarized, ] #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( na=3, nb=3, nc=50, ) left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=left_electrode_k_point_sampling, ) right_electrode_k_point_sampling = MonkhorstPackGrid( na=3, nb=3, nc=50, ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=right_electrode_k_point_sampling, ) device_k_point_sampling = MonkhorstPackGrid( na=3, nb=3, nc=50, ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=device_k_point_sampling, ) #---------------------------------------- # 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()]] ) #---------------------------------------- # Electrode Calculators #---------------------------------------- left_electrode_calculator = LCAOCalculator( basis_set=basis_set, numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters, poisson_solver=left_electrode_poisson_solver, ) right_electrode_calculator = LCAOCalculator( basis_set=basis_set, numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters, poisson_solver=right_electrode_poisson_solver, ) #---------------------------------------- # Device Calculator #---------------------------------------- calculator = DeviceLCAOCalculator( basis_set=basis_set, numerical_accuracy_parameters=device_numerical_accuracy_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) # ------------------------------------------------------------- # Device Density Of States # ------------------------------------------------------------- kpoint_grid = MonkhorstPackGrid( na=3, nb=3, ) device_density_of_states = DeviceDensityOfStates( configuration=device_configuration, energies=numpy.linspace(-3,3,401)*eV, kpoints=kpoint_grid, contributions=All, energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=RecursionSelfEnergy(), ) nlsave('au-dtb-au.nc', device_density_of_states) nlprint(device_density_of_states) # ------------------------------------------------------------- # Transmission Spectrum # ------------------------------------------------------------- kpoint_grid = MonkhorstPackGrid( na=3, nb=3, ) transmission_spectrum = TransmissionSpectrum( configuration=device_configuration, energies=numpy.linspace(-3,3,401)*eV, kpoints=kpoint_grid, energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=RecursionSelfEnergy(), ) nlsave('au-dtb-au.nc', transmission_spectrum) nlprint(transmission_spectrum)