# ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [2.866, 0.0, 0.0]*Angstrom vector_b = [0.0, 2.866, 0.0]*Angstrom vector_c = [0.0, 0.0, 5.732]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Iron, Iron, Iron, Iron] # Define coordinates left_electrode_coordinates = [[ 0.716500000003, 0.716500000003, 0.716499999992], [ 2.149500000003, 2.149500000003, 2.149500000008], [ 0.716500000003, 0.716500000003, 3.582499999992], [ 2.149500000003, 2.149500000003, 5.015500000008]]*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('Selection 0') # ------------------------------------------------------------- # Right Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [2.866, 0.0, 0.0]*Angstrom vector_b = [0.0, 2.866, 0.0]*Angstrom vector_c = [0.0, 0.0, 5.732]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Iron, Iron, Iron, Iron] # Define coordinates right_electrode_coordinates = [[ 0.716500000003, 0.716500000003, 0.716499999992], [ 2.149500000003, 2.149500000003, 2.149500000008], [ 0.716500000003, 0.716500000003, 3.582499999992], [ 2.149500000003, 2.149500000003, 5.015500000008]]*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('Selection 0') # ------------------------------------------------------------- # Central Region # ------------------------------------------------------------- # Set up lattice vector_a = [2.866, 0.0, 0.0]*Angstrom vector_b = [0.0, 2.866, 0.0]*Angstrom vector_c = [0.0, 0.0, 31.13975]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Iron, Iron, Iron, Iron, Iron, Iron, Magnesium, Oxygen, Oxygen, Magnesium, Magnesium, Oxygen, Oxygen, Magnesium, Magnesium, Oxygen, Oxygen, Magnesium, Iron, Iron, Iron, Iron, Iron, Iron] # Define coordinates central_region_coordinates = [[ 0.716500000003, 0.716500000003, 0.716499999992], [ 2.149500000003, 2.149500000003, 2.149500000008], [ 0.716500000003, 0.716500000003, 3.582499999992], [ 2.149500000003, 2.149500000003, 5.015500000008], [ 0.7165 , 0.7165 , 6.461176916299], [ 2.1495 , 2.1495 , 7.883348084818], [ 0.7165 , 0.7165 , 10.046913166035], [ 2.1495 , 2.1495 , 10.125854994682], [ 0.7165 , 0.7165 , 12.2742460054 ], [ 2.1495 , 2.1495 , 12.287565384199], [ 0.7165 , 0.7165 , 14.47251361208 ], [ 2.1495 , 2.1495 , 14.47501183558 ], [ 0.7165 , 0.7165 , 16.667197114 ], [ 2.1495 , 2.1495 , 16.669729913304], [ 0.7165 , 0.7165 , 18.854675912015], [ 2.1495 , 2.1495 , 18.867967064779], [ 0.7165 , 0.7165 , 21.016369375396], [ 2.1495 , 2.1495 , 21.095331583047], [ 0.7165 , 0.7165 , 23.258901803911], [ 2.1495 , 2.1495 , 24.681132523465], [ 0.716500000003, 0.716500000003, 26.124249999992], [ 2.149500000003, 2.149500000003, 27.557250000008], [ 0.716500000003, 0.716500000003, 28.990249999992], [ 2.149500000003, 2.149500000003, 30.423250000008]]*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('Selection 0', [0, 1, 2, 3, 20, 21, 22, 23]) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode] ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = [ GGABasis.Oxygen_DoubleZetaPolarized, GGABasis.Magnesium_DoubleZetaPolarized, GGABasis.Iron_SingleZetaPolarized, ] #---------------------------------------- # Exchange-Correlation #---------------------------------------- exchange_correlation = SGGA.PBE #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( electron_temperature=1200.0*Kelvin, k_point_sampling=left_electrode_k_point_sampling, ) right_electrode_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( electron_temperature=1200.0*Kelvin, k_point_sampling=right_electrode_k_point_sampling, ) device_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( electron_temperature=1200.0*Kelvin, 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, exchange_correlation=exchange_correlation, numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters, poisson_solver=left_electrode_poisson_solver, ) right_electrode_calculator = LCAOCalculator( basis_set=basis_set, exchange_correlation=exchange_correlation, numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters, poisson_solver=right_electrode_poisson_solver, ) #---------------------------------------- # Device Calculator #---------------------------------------- calculator = DeviceLCAOCalculator( basis_set=basis_set, exchange_correlation=exchange_correlation, numerical_accuracy_parameters=device_numerical_accuracy_parameters, electrode_calculators= [left_electrode_calculator, right_electrode_calculator], ) device_configuration.setCalculator(calculator) # ------------------------------------------------------------- # Initial State # ------------------------------------------------------------- initial_spin = InitialSpin(scaled_spins=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]) device_configuration.setCalculator( calculator, initial_spin=initial_spin, ) device_configuration.update() nlsave('mgo_para.nc', device_configuration) nlprint(device_configuration) # ------------------------------------------------------------- # Mulliken Population # ------------------------------------------------------------- mulliken_population = MullikenPopulation(device_configuration) nlsave('mgo_para.nc', mulliken_population) nlprint(mulliken_population) # ------------------------------------------------------------- # Forces # ------------------------------------------------------------- forces = Forces(device_configuration) nlsave('mgo_para.nc', forces) nlprint(forces) # ------------------------------------------------------------- # Transmission Spectrum # ------------------------------------------------------------- transmission_spectrum = TransmissionSpectrum( configuration=device_configuration, energies=numpy.linspace(0,0,1)*eV, kpoints=MonkhorstPackGrid(151,151), energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=RecursionSelfEnergy(), ) nlsave('mgo_para.nc', transmission_spectrum) nlprint(transmission_spectrum)