# -*- coding: utf-8 -*- for run in range(0,10): # ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [8.65127469112, 0.0, 0.0]*Angstrom vector_b = [0.0, 8.65127469112, 0.0]*Angstrom vector_c = [0.0, 0.0, 4.07825]*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] # Define coordinates left_electrode_coordinates = [[ 1.441879115187, 1.441879115187, 1.0195625 ], [ 4.325637345561, 1.441879115187, 1.0195625 ], [ 7.209395575935, 1.441879115187, 1.0195625 ], [ 1.441879115187, 4.325637345561, 1.0195625 ], [ 4.325637345561, 4.325637345561, 1.0195625 ], [ 7.209395575935, 4.325637345561, 1.0195625 ], [ 1.441879115187, 7.209395575935, 1.0195625 ], [ 4.325637345561, 7.209395575935, 1.0195625 ], [ 7.209395575935, 7.209395575935, 1.0195625 ], [ 0. , 0. , 3.0586875 ], [ 2.883758230374, 0. , 3.0586875 ], [ 5.767516460748, 0. , 3.0586875 ], [ 0. , 2.883758230374, 3.0586875 ], [ 2.883758230374, 2.883758230374, 3.0586875 ], [ 5.767516460748, 2.883758230374, 3.0586875 ], [ 0. , 5.767516460748, 3.0586875 ], [ 2.883758230374, 5.767516460748, 3.0586875 ], [ 5.767516460748, 5.767516460748, 3.0586875 ]]*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, 0.0, 0.0]*Angstrom vector_b = [0.0, 8.65127469112, 0.0]*Angstrom vector_c = [0.0, 0.0, 4.07825]*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] # Define coordinates right_electrode_coordinates = [[ 1.441879115187, 1.441879115187, 1.0195625 ], [ 4.325637345561, 1.441879115187, 1.0195625 ], [ 7.209395575935, 1.441879115187, 1.0195625 ], [ 1.441879115187, 4.325637345561, 1.0195625 ], [ 4.325637345561, 4.325637345561, 1.0195625 ], [ 7.209395575935, 4.325637345561, 1.0195625 ], [ 1.441879115187, 7.209395575935, 1.0195625 ], [ 4.325637345561, 7.209395575935, 1.0195625 ], [ 7.209395575935, 7.209395575935, 1.0195625 ], [ 0. , 0. , 3.0586875 ], [ 2.883758230374, 0. , 3.0586875 ], [ 5.767516460748, 0. , 3.0586875 ], [ 0. , 2.883758230374, 3.0586875 ], [ 2.883758230374, 2.883758230374, 3.0586875 ], [ 5.767516460748, 2.883758230374, 3.0586875 ], [ 0. , 5.767516460748, 3.0586875 ], [ 2.883758230374, 5.767516460748, 3.0586875 ], [ 5.767516460748, 5.767516460748, 3.0586875 ]]*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, 0.0, 0.0]*Angstrom vector_b = [0.0, 8.65127469112, 0.0]*Angstrom vector_c = [0.0, 0.0, 20.39125]*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, 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, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates central_region_coordinates = [[ 1.441879115187, 1.441879115187, 1.0195625 ], [ 4.325637345561, 1.441879115187, 1.0195625 ], [ 7.209395575935, 1.441879115187, 1.0195625 ], [ 1.441879115187, 4.325637345561, 1.0195625 ], [ 4.325637345561, 4.325637345561, 1.0195625 ], [ 7.209395575935, 4.325637345561, 1.0195625 ], [ 1.441879115187, 7.209395575935, 1.0195625 ], [ 4.325637345561, 7.209395575935, 1.0195625 ], [ 7.209395575935, 7.209395575935, 1.0195625 ], [ 0. , 0. , 3.0586875 ], [ 2.883758230374, 0. , 3.0586875 ], [ 5.767516460748, 0. , 3.0586875 ], [ 0. , 2.883758230374, 3.0586875 ], [ 2.883758230374, 2.883758230374, 3.0586875 ], [ 5.767516460748, 2.883758230374, 3.0586875 ], [ 0. , 5.767516460748, 3.0586875 ], [ 2.883758230374, 5.767516460748, 3.0586875 ], [ 5.767516460748, 5.767516460748, 3.0586875 ], [ 1.441879115187, 1.441879115187, 5.0978125 ], [ 4.325637345561, 1.441879115187, 5.0978125 ], [ 7.209395575935, 1.441879115187, 5.0978125 ], [ 1.441879115187, 4.325637345561, 5.0978125 ], [ 4.325637345561, 4.325637345561, 5.0978125 ], [ 7.209395575935, 4.325637345561, 5.0978125 ], [ 1.441879115187, 7.209395575935, 5.0978125 ], [ 4.325637345561, 7.209395575935, 5.0978125 ], [ 7.209395575935, 7.209395575935, 5.0978125 ], [ 0. , 0. , 7.1369375 ], [ 2.883758230374, 0. , 7.1369375 ], [ 5.767516460748, 0. , 7.1369375 ], [ 0. , 2.883758230374, 7.1369375 ], [ 2.883758230374, 2.883758230374, 7.1369375 ], [ 5.767516460748, 2.883758230374, 7.1369375 ], [ 0. , 5.767516460748, 7.1369375 ], [ 2.883758230374, 5.767516460748, 7.1369375 ], [ 5.767516460748, 5.767516460748, 7.1369375 ], [ 1.441879115187, 1.441879115187, 9.1760625 ], [ 4.325637345561, 1.441879115187, 9.1760625 ], [ 7.209395575935, 1.441879115187, 9.1760625 ], [ 1.441879115187, 4.325637345561, 9.1760625 ], [ 4.325637345561, 4.325637345561, 9.1760625 ], [ 7.209395575935, 4.325637345561, 9.1760625 ], [ 1.441879115187, 7.209395575935, 9.1760625 ], [ 4.325637345561, 7.209395575935, 9.1760625 ], [ 7.209395575935, 7.209395575935, 9.1760625 ], [ 0. , 0. , 11.2151875 ], [ 2.883758230374, 0. , 11.2151875 ], [ 5.767516460748, 0. , 11.2151875 ], [ 0. , 2.883758230374, 11.2151875 ], [ 2.883758230374, 2.883758230374, 11.2151875 ], [ 5.767516460748, 2.883758230374, 11.2151875 ], [ 0. , 5.767516460748, 11.2151875 ], [ 2.883758230374, 5.767516460748, 11.2151875 ], [ 5.767516460748, 5.767516460748, 11.2151875 ], [ 1.441879115187, 1.441879115187, 13.2543125 ], [ 4.325637345561, 1.441879115187, 13.2543125 ], [ 7.209395575935, 1.441879115187, 13.2543125 ], [ 1.441879115187, 4.325637345561, 13.2543125 ], [ 4.325637345561, 4.325637345561, 13.2543125 ], [ 7.209395575935, 4.325637345561, 13.2543125 ], [ 1.441879115187, 7.209395575935, 13.2543125 ], [ 4.325637345561, 7.209395575935, 13.2543125 ], [ 7.209395575935, 7.209395575935, 13.2543125 ], [ 0. , 0. , 15.2934375 ], [ 2.883758230374, 0. , 15.2934375 ], [ 5.767516460748, 0. , 15.2934375 ], [ 0. , 2.883758230374, 15.2934375 ], [ 2.883758230374, 2.883758230374, 15.2934375 ], [ 5.767516460748, 2.883758230374, 15.2934375 ], [ 0. , 5.767516460748, 15.2934375 ], [ 2.883758230374, 5.767516460748, 15.2934375 ], [ 5.767516460748, 5.767516460748, 15.2934375 ], [ 1.441879115187, 1.441879115187, 17.3325625 ], [ 4.325637345561, 1.441879115187, 17.3325625 ], [ 7.209395575935, 1.441879115187, 17.3325625 ], [ 1.441879115187, 4.325637345561, 17.3325625 ], [ 4.325637345561, 4.325637345561, 17.3325625 ], [ 7.209395575935, 4.325637345561, 17.3325625 ], [ 1.441879115187, 7.209395575935, 17.3325625 ], [ 4.325637345561, 7.209395575935, 17.3325625 ], [ 7.209395575935, 7.209395575935, 17.3325625 ], [ 0. , 0. , 19.3716875 ], [ 2.883758230374, 0. , 19.3716875 ], [ 5.767516460748, 0. , 19.3716875 ], [ 0. , 2.883758230374, 19.3716875 ], [ 2.883758230374, 2.883758230374, 19.3716875 ], [ 5.767516460748, 2.883758230374, 19.3716875 ], [ 0. , 5.767516460748, 19.3716875 ], [ 2.883758230374, 5.767516460748, 19.3716875 ], [ 5.767516460748, 5.767516460748, 19.3716875 ]]*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 # ------------------------------------------------------------- potentialSet = EAM_Au_Sheng_2011() calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(0.25*Angstrom) device_configuration.setCalculator(calculator) nlprint(device_configuration) device_configuration.update() nlsave('Au100_L3_T300.nc', device_configuration) # ------------------------------------------------------------- # Molecular Dynamics # ------------------------------------------------------------- initial_velocity = MaxwellBoltzmannDistribution( temperature=300.0*Kelvin, remove_center_of_mass_momentum=True ) method = Langevin( time_step=1*femtoSecond, reservoir_temperature=300*Kelvin, friction=0.01*femtoSecond**-1, initial_velocity=initial_velocity, heating_rate=0*Kelvin/picoSecond, ) md_trajectory = MolecularDynamics( device_configuration, constraints=[], trajectory_filename='trajectory.nc', steps=5000, log_interval=100, method=method ) device_configuration = md_trajectory.lastImage() nlsave('Au100_L3_T300.nc', md_trajectory) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = HotbitDirectory("hotbit/standard/") #---------------------------------------- # Pair Potentials #---------------------------------------- pair_potentials = HotbitDirectory("hotbit/standard/") #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( na=2, nb=2, nc=42, ) left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=left_electrode_k_point_sampling, ) right_electrode_k_point_sampling = MonkhorstPackGrid( na=2, nb=2, nc=42, ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=right_electrode_k_point_sampling, ) device_k_point_sampling = MonkhorstPackGrid( na=2, nb=2, nc=42, ) 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()]] ) #---------------------------------------- # Electrode Calculators #---------------------------------------- left_electrode_calculator = SlaterKosterCalculator( basis_set=basis_set, pair_potentials=pair_potentials, 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, pair_potentials=pair_potentials, 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, pair_potentials=pair_potentials, numerical_accuracy_parameters=device_numerical_accuracy_parameters, iteration_control_parameters=device_iteration_control_parameters, electrode_calculators= [left_electrode_calculator, right_electrode_calculator], ) device_configuration.setCalculator(calculator) nlprint(device_configuration) device_configuration.update() nlsave('Au100_L3_T300.nc', device_configuration) # ------------------------------------------------------------- # Transmission Spectrum # ------------------------------------------------------------- kpoint_grid = MonkhorstPackGrid( na=10, nb=10, ) transmission_spectrum = TransmissionSpectrum( configuration=device_configuration, energies=numpy.linspace(-0.2,0.2,51)*eV, kpoints=kpoint_grid, energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=KrylovSelfEnergy(), ) nlsave('Au100_L3_T300.nc', transmission_spectrum) nlprint(transmission_spectrum)