# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [10.0, 0.0, 0.0]*Angstrom vector_b = [0.0, 25.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 7.38300513133]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon] # Define coordinates left_electrode_coordinates = [[ 5. , 5.750915 , 0.615250427611], [ 5. , 8.592635 , 0.615250427611], [ 5. , 17.117795 , 0.615250427611], [ 5. , 18.538655 , 0.615250427611], [ 5. , 6.461345 , 1.845751282832], [ 5. , 7.882205 , 1.845751282832], [ 5. , 16.407365 , 1.845751282832], [ 5. , 19.249085 , 1.845751282832], [ 5. , 5.750915 , 3.076252138053], [ 5. , 8.592635 , 3.076252138053], [ 5. , 17.117795 , 3.076252138053], [ 5. , 18.538655 , 3.076252138053], [ 5. , 6.461345 , 4.306752993274], [ 5. , 7.882205 , 4.306752993274], [ 5. , 16.407365 , 4.306752993274], [ 5. , 19.249085 , 4.306752993274], [ 5. , 5.750915 , 5.537253848495], [ 5. , 8.592635 , 5.537253848495], [ 5. , 17.117795 , 5.537253848495], [ 5. , 18.538655 , 5.537253848495], [ 5. , 6.461345 , 6.767754703716], [ 5. , 7.882205 , 6.767754703716], [ 5. , 16.407365 , 6.767754703716], [ 5. , 19.249085 , 6.767754703716]]*Angstrom # Set up configuration left_electrode = BulkConfiguration( bravais_lattice=left_electrode_lattice, elements=left_electrode_elements, cartesian_coordinates=left_electrode_coordinates ) # Add tags left_electrode.addTags('lead1', [2, 3, 6, 7, 10, 11, 14, 15, 18, 19, 22, 23]) left_electrode.addTags('lead2', [0, 1, 4, 5, 8, 9, 12, 13, 16, 17, 20, 21]) # ------------------------------------------------------------- # Right Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [10.0, 0.0, 0.0]*Angstrom vector_b = [0.0, 25.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 7.38300513133]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon] # Define coordinates right_electrode_coordinates = [[ 5. , 5.750915 , 0.615250427611], [ 5. , 8.592635 , 0.615250427611], [ 5. , 17.117795 , 0.615250427611], [ 5. , 18.538655 , 0.615250427611], [ 5. , 6.461345 , 1.845751282832], [ 5. , 7.882205 , 1.845751282832], [ 5. , 16.407365 , 1.845751282832], [ 5. , 19.249085 , 1.845751282832], [ 5. , 5.750915 , 3.076252138053], [ 5. , 8.592635 , 3.076252138053], [ 5. , 17.117795 , 3.076252138053], [ 5. , 18.538655 , 3.076252138053], [ 5. , 6.461345 , 4.306752993274], [ 5. , 7.882205 , 4.306752993274], [ 5. , 16.407365 , 4.306752993274], [ 5. , 19.249085 , 4.306752993274], [ 5. , 5.750915 , 5.537253848495], [ 5. , 8.592635 , 5.537253848495], [ 5. , 17.117795 , 5.537253848495], [ 5. , 18.538655 , 5.537253848495], [ 5. , 6.461345 , 6.767754703716], [ 5. , 7.882205 , 6.767754703716], [ 5. , 16.407365 , 6.767754703716], [ 5. , 19.249085 , 6.767754703716]]*Angstrom # Set up configuration right_electrode = BulkConfiguration( bravais_lattice=right_electrode_lattice, elements=right_electrode_elements, cartesian_coordinates=right_electrode_coordinates ) # Add tags right_electrode.addTags('lead3', [2, 3, 6, 7, 10, 11, 14, 15, 18, 19, 22, 23]) right_electrode.addTags('lead4', [0, 1, 4, 5, 8, 9, 12, 13, 16, 17, 20, 21]) # ------------------------------------------------------------- # Central Region # ------------------------------------------------------------- # Set up lattice vector_a = [10.0, 0.0, 0.0]*Angstrom vector_b = [0.0, 25.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 29.5320205253]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon] # Define coordinates central_region_coordinates = [[ 5. , 5.750915 , 0.615250427611], [ 5. , 8.592635 , 0.615250427611], [ 5. , 17.117795 , 0.615250427611], [ 5. , 18.538655 , 0.615250427611], [ 5. , 6.461345 , 1.845751282832], [ 5. , 7.882205 , 1.845751282832], [ 5. , 16.407365 , 1.845751282832], [ 5. , 19.249085 , 1.845751282832], [ 5. , 5.750915 , 3.076252138053], [ 5. , 8.592635 , 3.076252138053], [ 5. , 17.117795 , 3.076252138053], [ 5. , 18.538655 , 3.076252138053], [ 5. , 6.461345 , 4.306752993274], [ 5. , 7.882205 , 4.306752993274], [ 5. , 16.407365 , 4.306752993274], [ 5. , 19.249085 , 4.306752993274], [ 5. , 5.750915 , 5.537253848495], [ 5. , 8.592635 , 5.537253848495], [ 5. , 17.117795 , 5.537253848495], [ 5. , 18.538655 , 5.537253848495], [ 5. , 6.461345 , 6.767754703716], [ 5. , 7.882205 , 6.767754703716], [ 5. , 16.407365 , 6.767754703716], [ 5. , 19.249085 , 6.767754703716], [ 5. , 5.750915 , 7.998255558938], [ 5. , 8.592635 , 7.998255558938], [ 5. , 17.117795 , 7.998255558938], [ 5. , 18.538655 , 7.998255558938], [ 5. , 6.461345 , 9.228756414159], [ 5. , 7.882205 , 9.228756414159], [ 5. , 10.723925 , 9.228756414159], [ 5. , 12.144785 , 9.228756414159], [ 5. , 14.986505 , 9.228756414159], [ 5. , 16.407365 , 9.228756414159], [ 5. , 19.249085 , 9.228756414159], [ 5. , 5.750915 , 10.45925726938 ], [ 5. , 8.592635 , 10.45925726938 ], [ 5. , 10.013495 , 10.45925726938 ], [ 5. , 12.855215 , 10.45925726938 ], [ 5. , 14.276075 , 10.45925726938 ], [ 5. , 17.117795 , 10.45925726938 ], [ 5. , 18.538655 , 10.45925726938 ], [ 5. , 6.461345 , 11.689758124601], [ 5. , 7.882205 , 11.689758124601], [ 5. , 10.723925 , 11.689758124601], [ 5. , 12.144785 , 11.689758124601], [ 5. , 14.986505 , 11.689758124601], [ 5. , 16.407365 , 11.689758124601], [ 5. , 19.249085 , 11.689758124601], [ 5. , 14.257883546055, 12.773287892691], [ 5. , 12.873406454041, 12.773287892982], [ 5. , 5.750915 , 12.920258979822], [ 5. , 8.592635 , 12.920258979822], [ 5. , 10.013495 , 12.920258979822], [ 5. , 17.117795 , 12.920258979822], [ 5. , 18.538655 , 12.920258979822], [ 5. , 12.19456505321 , 14.030708696767], [ 5. , 14.936724946796, 14.030708696776], [ 5. , 6.461345 , 14.150759835043], [ 5. , 7.882205 , 14.150759835043], [ 5. , 10.723925 , 14.150759835043], [ 5. , 16.407365 , 14.150759835043], [ 5. , 19.249085 , 14.150759835043], [ 5. , 13.565644999904, 14.750691998909], [ 5. , 5.750915 , 15.381260690264], [ 5. , 8.592635 , 15.381260690264], [ 5. , 10.013495 , 15.381260690264], [ 5. , 17.117795 , 15.381260690264], [ 5. , 18.538655 , 15.381260690264], [ 5. , 13.565645000211, 16.011829097332], [ 5. , 6.461345 , 16.611761545486], [ 5. , 7.882205 , 16.611761545486], [ 5. , 10.723925 , 16.611761545486], [ 5. , 16.407365 , 16.611761545486], [ 5. , 19.249085 , 16.611761545486], [ 5. , 12.194565051441, 16.7318126837 ], [ 5. , 14.936724948547, 16.731812683718], [ 5. , 5.750915 , 17.842262400707], [ 5. , 8.592635 , 17.842262400707], [ 5. , 10.013495 , 17.842262400707], [ 5. , 17.117795 , 17.842262400707], [ 5. , 18.538655 , 17.842262400707], [ 5. , 14.257883594282, 17.989233630584], [ 5. , 12.873406405504, 17.989233631238], [ 5. , 6.461345 , 19.072763255928], [ 5. , 7.882205 , 19.072763255928], [ 5. , 10.723925 , 19.072763255928], [ 5. , 12.144785 , 19.072763255928], [ 5. , 14.986505 , 19.072763255928], [ 5. , 16.407365 , 19.072763255928], [ 5. , 19.249085 , 19.072763255928], [ 5. , 5.750915 , 20.303264111149], [ 5. , 8.592635 , 20.303264111149], [ 5. , 10.013495 , 20.303264111149], [ 5. , 12.855215 , 20.303264111149], [ 5. , 14.276075 , 20.303264111149], [ 5. , 17.117795 , 20.303264111149], [ 5. , 18.538655 , 20.303264111149], [ 5. , 6.461345 , 21.53376496637 ], [ 5. , 7.882205 , 21.53376496637 ], [ 5. , 10.723925 , 21.53376496637 ], [ 5. , 12.144785 , 21.53376496637 ], [ 5. , 14.986505 , 21.53376496637 ], [ 5. , 16.407365 , 21.53376496637 ], [ 5. , 19.249085 , 21.53376496637 ], [ 5. , 5.750915 , 22.764265821591], [ 5. , 8.592635 , 22.764265821591], [ 5. , 17.117795 , 22.764265821591], [ 5. , 18.538655 , 22.764265821591], [ 5. , 6.461345 , 23.994766676813], [ 5. , 7.882205 , 23.994766676813], [ 5. , 16.407365 , 23.994766676813], [ 5. , 19.249085 , 23.994766676813], [ 5. , 5.750915 , 25.225267532034], [ 5. , 8.592635 , 25.225267532034], [ 5. , 17.117795 , 25.225267532034], [ 5. , 18.538655 , 25.225267532034], [ 5. , 6.461345 , 26.455768387255], [ 5. , 7.882205 , 26.455768387255], [ 5. , 16.407365 , 26.455768387255], [ 5. , 19.249085 , 26.455768387255], [ 5. , 5.750915 , 27.686269242476], [ 5. , 8.592635 , 27.686269242476], [ 5. , 17.117795 , 27.686269242476], [ 5. , 18.538655 , 27.686269242476], [ 5. , 6.461345 , 28.916770097697], [ 5. , 7.882205 , 28.916770097697], [ 5. , 16.407365 , 28.916770097697], [ 5. , 19.249085 , 28.916770097697]]*Angstrom # Set up configuration central_region = BulkConfiguration( bravais_lattice=central_region_lattice, elements=central_region_elements, cartesian_coordinates=central_region_coordinates ) # Add tags central_region.addTags('lead1', [2, 3, 6, 7, 10, 11, 14, 15, 18, 19, 22, 23]) central_region.addTags('lead2', [0, 1, 4, 5, 8, 9, 12, 13, 16, 17, 20, 21]) central_region.addTags('lead3', [107, 108, 111, 112, 115, 116, 119, 120, 123, 124, 127, 128]) central_region.addTags('lead4', [105, 106, 109, 110, 113, 114, 117, 118, 121, 122, 125, 126]) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode] ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = Hancock.C_Basis #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( shift_to_gamma=(False, False, False), na=1, nb=1, 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=1, nb=1, 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=1, nb=1, nc=100, ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=device_k_point_sampling, ) #---------------------------------------- # Iteration Control Settings #---------------------------------------- left_electrode_iteration_control_parameters = IterationControlParameters( tolerance=0.0001, ) right_electrode_iteration_control_parameters = IterationControlParameters( tolerance=0.0001, ) #---------------------------------------- # 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 = SlaterKosterCalculator( 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 = SlaterKosterCalculator( 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 = DeviceSlaterKosterCalculator( basis_set=basis_set, numerical_accuracy_parameters=device_numerical_accuracy_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('4probe_pi_model.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(0,0,1)*eV, kpoints=kpoint_grid, energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=RecursionSelfEnergy(), ) nlsave('4probe_pi_model.nc', transmission_spectrum) nlprint(transmission_spectrum)