# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [3.84001408591, 0.0, 0.0]*Angstrom vector_b = [0.0, 3.84001408591, 0.0]*Angstrom vector_c = [0.0, 0.0, 5.4306]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Silicon, Silicon, Silicon, Silicon] # Define coordinates left_electrode_coordinates = [[ 1.920007042956, 0. , 0.678625 ], [ 1.920007042956, 1.920007042956, 2.036275 ], [ 0. , 1.920007042956, 3.393925 ], [ 0. , 0. , 4.751575 ]]*Angstrom # Set up configuration left_electrode = BulkConfiguration( bravais_lattice=left_electrode_lattice, elements=left_electrode_elements, cartesian_coordinates=left_electrode_coordinates ) # Add external potential external_potential = AtomicCompensationCharge([ (Silicon, -0.000400390214211) ]) left_electrode.setExternalPotential(external_potential) # ------------------------------------------------------------- # Right Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [3.84001408591, 0.0, 0.0]*Angstrom vector_b = [0.0, 3.84001408591, 0.0]*Angstrom vector_c = [0.0, 0.0, 5.4306]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Silicon, Silicon, Silicon, Silicon] # Define coordinates right_electrode_coordinates = [[ 1.920007042956, 0. , 0.679025 ], [ 1.920007042956, 1.920007042956, 2.036675 ], [ 0. , 1.920007042956, 3.394325 ], [ 0. , 0. , 4.751975 ]]*Angstrom # Set up configuration right_electrode = BulkConfiguration( bravais_lattice=right_electrode_lattice, elements=right_electrode_elements, cartesian_coordinates=right_electrode_coordinates ) # Add external potential external_potential = AtomicCompensationCharge([ (Silicon, 0.000400390214211) ]) right_electrode.setExternalPotential(external_potential) # ------------------------------------------------------------- # Central Region # ------------------------------------------------------------- # Set up lattice vector_a = [3.84001408591, 0.0, 0.0]*Angstrom vector_b = [0.0, 3.84001408591, 0.0]*Angstrom vector_c = [0.0, 0.0, 65.1668]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon] # Define coordinates central_region_coordinates = [[ 1.920007042956, 0. , 0.678625 ], [ 1.920007042956, 1.920007042956, 2.036275 ], [ 0. , 1.920007042956, 3.393925 ], [ 0. , 0. , 4.751575 ], [ 1.920007042956, 0. , 6.109225 ], [ 1.920007042956, 1.920007042956, 7.466875 ], [ 0. , 1.920007042956, 8.824525 ], [ 0. , 0. , 10.182175 ], [ 1.920007042956, 0. , 11.539825 ], [ 1.920007042956, 1.920007042956, 12.897475 ], [ 0. , 1.920007042956, 14.255125 ], [ 0. , 0. , 15.612775 ], [ 1.920007042956, 0. , 16.970425 ], [ 1.920007042956, 1.920007042956, 18.328075 ], [ 0. , 1.920007042956, 19.685725 ], [ 0. , 0. , 21.043375 ], [ 1.920007042956, 0. , 22.401025 ], [ 1.920007042956, 1.920007042956, 23.758675 ], [ 0. , 1.920007042956, 25.116325 ], [ 0. , 0. , 26.473975 ], [ 1.920007042956, 0. , 27.831625 ], [ 1.920007042956, 1.920007042956, 29.189275 ], [ 0. , 1.920007042956, 30.546925 ], [ 0. , 0. , 31.904575 ], [ 1.920007042956, 0. , 33.262225 ], [ 1.920007042956, 1.920007042956, 34.619875 ], [ 0. , 1.920007042956, 35.977525 ], [ 0. , 0. , 37.335175 ], [ 1.920007042956, 0. , 38.692825 ], [ 1.920007042956, 1.920007042956, 40.050475 ], [ 0. , 1.920007042956, 41.408125 ], [ 0. , 0. , 42.765775 ], [ 1.920007042956, 0. , 44.123425 ], [ 1.920007042956, 1.920007042956, 45.481075 ], [ 0. , 1.920007042956, 46.838725 ], [ 0. , 0. , 48.196375 ], [ 1.920007042956, 0. , 49.554025 ], [ 1.920007042956, 1.920007042956, 50.911675 ], [ 0. , 1.920007042956, 52.269325 ], [ 0. , 0. , 53.626975 ], [ 1.920007042956, 0. , 54.984625 ], [ 1.920007042956, 1.920007042956, 56.342275 ], [ 0. , 1.920007042956, 57.699925 ], [ 0. , 0. , 59.057575 ], [ 1.920007042956, 0. , 60.415225 ], [ 1.920007042956, 1.920007042956, 61.772875 ], [ 0. , 1.920007042956, 63.130525 ], [ 0. , 0. , 64.488175 ]]*Angstrom # Set up configuration central_region = BulkConfiguration( bravais_lattice=central_region_lattice, elements=central_region_elements, cartesian_coordinates=central_region_coordinates ) # Add external potential external_potential = AtomicCompensationCharge([ ('doping_0', -0.000400390214211), ('doping_1', 0.000400390214211) ]) central_region.setExternalPotential(external_potential) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode] ) # Add tags device_configuration.addTags('doping_0', [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) device_configuration.addTags('doping_1', [24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- hydrogen_onsite_term = SlaterKosterOnsiteParameters( element=PeriodicTable.Hydrogen, angular_momenta=[ 0 ], occupations=[ 1.0 ], filling_method=SphericalSymmetric, ionization_potential=[ 0.6*eV ], onsite_hartree_shift=[ 10.89*eV ], onsite_spin_split=[[0.0]]*eV, onsite_spin_orbit_split=[0.0]*eV, vacuum_level=0.0*Hartree, ) silicon_onsite_term = SlaterKosterOnsiteParameters( element=PeriodicTable.Silicon, angular_momenta=[ 0 , 1 , 0 ], occupations=[ 1.239 , 2.679 , 0.082 ], filling_method=SphericalSymmetric, ionization_potential=[ -4.2*eV , 1.715*eV , 6.685*eV ], onsite_hartree_shift=[ 7.1173688*eV , 7.1173688*eV , 7.1173688*eV ], onsite_spin_split=[[-0.5613, -0.43065, -0.5613], [-0.43065, -0.3727, -0.43065], [-0.5613, -0.43065, -0.5613]]*eV, onsite_spin_orbit_split=[0.0, 0.02933333333333333, 0.0]*eV, vacuum_level=0.0*Hartree, ) basis_set = SlaterKosterTable( hydrogen=hydrogen_onsite_term, silicon=silicon_onsite_term, h_si_sss=[ (1.36*Angstrom, -3.5*eV), (1.394*Angstrom, -3.5*eV), (1.428*Angstrom, -3.5*eV), (1.462*Angstrom, -3.5*eV), (1.496*Angstrom, -3.5*eV), (1.53*Angstrom, -3.5*eV), (1.564*Angstrom, -3.5*eV), (1.598*Angstrom, -3.5*eV), (1.632*Angstrom, -3.5*eV), (1.666*Angstrom, -3.5*eV), (1.7*Angstrom, -3.5*eV), (1.734*Angstrom, -3.5*eV), (1.768*Angstrom, -3.5*eV), (1.802*Angstrom, -3.5*eV), (1.836*Angstrom, -3.5*eV), (1.87*Angstrom, -3.5*eV), (1.904*Angstrom, -3.5*eV), (1.938*Angstrom, -3.5*eV), (1.972*Angstrom, -3.5*eV), (2.006*Angstrom, -3.5*eV), (2.04*Angstrom, -3.5*eV), (2.2*Angstrom, 0.0*eV), ], si_si_sps=[ (2.11613307415*Angstrom, 3.06273626133*eV), (2.13964566386*Angstrom, 2.99579322749*eV), (2.16315825357*Angstrom, 2.93102123308*eV), (2.18667084329*Angstrom, 2.86832740396*eV), (2.210183433*Angstrom, 2.80762377963*eV), (2.23369602271*Angstrom, 2.74882700463*eV), (2.25720861242*Angstrom, 2.69185804219*eV), (2.28072120214*Angstrom, 2.63664190847*eV), (2.30423379185*Angstrom, 2.58310742574*eV), (2.32774638156*Angstrom, 2.53118699284*eV), (2.35125897127*Angstrom, 2.48081637168*eV), (2.37477156099*Angstrom, 2.43193448846*eV), (2.3982841507*Angstrom, 2.38448324844*eV), (2.42179674041*Angstrom, 2.33840736326*eV), (2.44530933013*Angstrom, 2.29365418979*eV), (2.46882191984*Angstrom, 2.25017357976*eV), (2.49233450955*Angstrom, 2.20791773913*eV), (2.51584709926*Angstrom, 2.16684109676*eV), (2.53935968898*Angstrom, 2.12690018148*eV), (2.56287227869*Angstrom, 2.08805350701*eV), (2.5863848684*Angstrom, 2.0502614642*eV), (3.09542439656*Angstrom, 0.0*eV), ], h_si_sps=[ (1.36*Angstrom, 4.5*eV), (1.394*Angstrom, 4.5*eV), (1.428*Angstrom, 4.5*eV), (1.462*Angstrom, 4.5*eV), (1.496*Angstrom, 4.5*eV), (1.53*Angstrom, 4.5*eV), (1.564*Angstrom, 4.5*eV), (1.598*Angstrom, 4.5*eV), (1.632*Angstrom, 4.5*eV), (1.666*Angstrom, 4.5*eV), (1.7*Angstrom, 4.5*eV), (1.734*Angstrom, 4.5*eV), (1.768*Angstrom, 4.5*eV), (1.802*Angstrom, 4.5*eV), (1.836*Angstrom, 4.5*eV), (1.87*Angstrom, 4.5*eV), (1.904*Angstrom, 4.5*eV), (1.938*Angstrom, 4.5*eV), (1.972*Angstrom, 4.5*eV), (2.006*Angstrom, 4.5*eV), (2.04*Angstrom, 4.5*eV), (2.2*Angstrom, 0.0*eV), ], h_si_ss1s=[ (1.36*Angstrom, 0.0*eV), (1.394*Angstrom, 0.0*eV), (1.428*Angstrom, 0.0*eV), (1.462*Angstrom, 0.0*eV), (1.496*Angstrom, 0.0*eV), (1.53*Angstrom, 0.0*eV), (1.564*Angstrom, 0.0*eV), (1.598*Angstrom, 0.0*eV), (1.632*Angstrom, 0.0*eV), (1.666*Angstrom, 0.0*eV), (1.7*Angstrom, 0.0*eV), (1.734*Angstrom, 0.0*eV), (1.768*Angstrom, 0.0*eV), (1.802*Angstrom, 0.0*eV), (1.836*Angstrom, 0.0*eV), (1.87*Angstrom, 0.0*eV), (1.904*Angstrom, 0.0*eV), (1.938*Angstrom, 0.0*eV), (1.972*Angstrom, 0.0*eV), (2.006*Angstrom, 0.0*eV), (2.04*Angstrom, 0.0*eV), (2.2*Angstrom, 0.0*eV), ], si_si_ps1s=[ (2.11613307415*Angstrom, 2.87333329803*eV), (2.13964566386*Angstrom, 2.81053009468*eV), (2.16315825357*Angstrom, 2.74976367131*eV), (2.18667084329*Angstrom, 2.69094689721*eV), (2.210183433*Angstrom, 2.63399725147*eV), (2.23369602271*Angstrom, 2.57883653341*eV), (2.25720861242*Angstrom, 2.52539059397*eV), (2.28072120214*Angstrom, 2.47358908641*eV), (2.30423379185*Angstrom, 2.42336523469*eV), (2.32774638156*Angstrom, 2.3746556182*eV), (2.35125897127*Angstrom, 2.3273999714*eV), (2.37477156099*Angstrom, 2.28154099735*eV), (2.3982841507*Angstrom, 2.23702419396*eV), (2.42179674041*Angstrom, 2.19379769196*eV), (2.44530933013*Angstrom, 2.15181210374*eV), (2.46882191984*Angstrom, 2.11102038222*eV), (2.49233450955*Angstrom, 2.07137768904*eV), (2.51584709926*Angstrom, 2.0328412712*eV), (2.53935968898*Angstrom, 1.99537034585*eV), (2.56287227869*Angstrom, 1.95892599226*eV), (2.5863848684*Angstrom, 1.92347105074*eV), (3.09542439656*Angstrom, 0.0*eV), ], si_si_pps=[ (2.11613307415*Angstrom, 3.35339506173*eV), (2.13964566386*Angstrom, 3.28009902186*eV), (2.16315825357*Angstrom, 3.20918005671*eV), (2.18667084329*Angstrom, 3.14053647821*eV), (2.210183433*Angstrom, 3.07407197827*eV), (2.23369602271*Angstrom, 3.00969529086*eV), (2.25720861242*Angstrom, 2.94731987847*eV), (2.28072120214*Angstrom, 2.88686364119*eV), (2.30423379185*Angstrom, 2.8282486464*eV), (2.32774638156*Angstrom, 2.77140087746*eV), (2.35125897127*Angstrom, 2.71625*eV), (2.37477156099*Angstrom, 2.6627291442*eV), (2.3982841507*Angstrom, 2.61077470204*eV), (2.42179674041*Angstrom, 2.56032613818*eV), (2.44530933013*Angstrom, 2.51132581361*eV), (2.46882191984*Angstrom, 2.46371882086*eV), (2.49233450955*Angstrom, 2.41745283019*eV), (2.51584709926*Angstrom, 2.37247794567*eV), (2.53935968898*Angstrom, 2.32874657064*eV), (2.56287227869*Angstrom, 2.28621328171*eV), (2.5863848684*Angstrom, 2.24483471074*eV), (3.09542439656*Angstrom, 0.0*eV), ], si_si_ppp=[ (2.11613307415*Angstrom, -0.882716049383*eV), (2.13964566386*Angstrom, -0.863422291994*eV), (2.16315825357*Angstrom, -0.844754253308*eV), (2.18667084329*Angstrom, -0.826685165915*eV), (2.210183433*Angstrom, -0.809189678588*eV), (2.23369602271*Angstrom, -0.792243767313*eV), (2.25720861242*Angstrom, -0.775824652778*eV), (2.28072120214*Angstrom, -0.759910723775*eV), (2.30423379185*Angstrom, -0.744481466056*eV), (2.32774638156*Angstrom, -0.729517396184*eV), (2.35125897127*Angstrom, -0.715*eV), (2.37477156099*Angstrom, -0.700911675326*eV), (2.3982841507*Angstrom, -0.687235678585*eV), (2.42179674041*Angstrom, -0.673956075031*eV), (2.44530933013*Angstrom, -0.661057692308*eV), (2.46882191984*Angstrom, -0.648526077098*eV), (2.49233450955*Angstrom, -0.63634745461*eV), (2.51584709926*Angstrom, -0.624508690715*eV), (2.53935968898*Angstrom, -0.612997256516*eV), (2.56287227869*Angstrom, -0.601801195186*eV), (2.5863848684*Angstrom, -0.590909090909*eV), (3.09542439656*Angstrom, 0.0*eV), ], si_si_sss=[ (2.11613307415*Angstrom, -2.56172839506*eV), (2.13964566386*Angstrom, -2.50573602222*eV), (2.16315825357*Angstrom, -2.45155954631*eV), (2.18667084329*Angstrom, -2.3991212857*eV), (2.210183433*Angstrom, -2.34834766863*eV), (2.23369602271*Angstrom, -2.29916897507*eV), (2.25720861242*Angstrom, -2.25151909722*eV), (2.28072120214*Angstrom, -2.20533531725*eV), (2.30423379185*Angstrom, -2.16055810079*eV), (2.32774638156*Angstrom, -2.11713090501*eV), (2.35125897127*Angstrom, -2.075*eV), (2.37477156099*Angstrom, -2.03411430252*eV), (2.3982841507*Angstrom, -1.99442522107*eV), (2.42179674041*Angstrom, -1.95588651145*eV), (2.44530933013*Angstrom, -1.91845414201*eV), (2.46882191984*Angstrom, -1.8820861678*eV), (2.49233450955*Angstrom, -1.84674261303*eV), (2.51584709926*Angstrom, -1.81238536117*eV), (2.53935968898*Angstrom, -1.77897805213*eV), (2.56287227869*Angstrom, -1.74648598603*eV), (2.5863848684*Angstrom, -1.71487603306*eV), (3.09542439656*Angstrom, 0.0*eV), ], ) #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=left_electrode_k_point_sampling, density_mesh_cutoff=10.0*Hartree, ) right_electrode_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=right_electrode_k_point_sampling, density_mesh_cutoff=10.0*Hartree, ) device_k_point_sampling = MonkhorstPackGrid( na=7, nb=7, nc=100, ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=device_k_point_sampling, density_mesh_cutoff=10.0*Hartree, ) #---------------------------------------- # Iteration Control Settings #---------------------------------------- left_electrode_iteration_control_parameters = IterationControlParameters( tolerance=4e-05, ) right_electrode_iteration_control_parameters = IterationControlParameters( tolerance=4e-05, ) device_iteration_control_parameters = IterationControlParameters( tolerance=4e-05, ) #---------------------------------------- # 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()]] ) #---------------------------------------- # Contour Integral Settings #---------------------------------------- non_equilibrium_contour = RealAxisContour( real_axis_point_density=0.0001*Hartree, real_axis_infinitesimal=0.0001*Hartree, ) contour_parameters = ContourParameters( non_equilibrium_contour=non_equilibrium_contour, ) #---------------------------------------- # 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, iteration_control_parameters=device_iteration_control_parameters, contour_parameters=contour_parameters, electrode_calculators= [left_electrode_calculator, right_electrode_calculator], electrode_voltages=( -0.2*Volt, 0.2*Volt), ) device_configuration.setCalculator(calculator) nlprint(device_configuration) device_configuration.update() nlsave('xloe_V-0.4_bulk.hdf5', device_configuration) # ------------------------------------------------------------- # Dynamical Matrix # ------------------------------------------------------------- dynamical_matrix = nlread('dynmat_bulk.hdf5',DynamicalMatrix)[-1] # ------------------------------------------------------------- # Hamiltonian Derivatives # ------------------------------------------------------------- hamiltonian_derivatives = nlread('dHdR_bulk.hdf5',HamiltonianDerivatives)[-1] # ------------------------------------------------------------- # Inelastic Transmission Spectrum # ------------------------------------------------------------- kpoints = RegularKpointGrid( ka_range=[-0.2, 0.2], kb_range=[-0.2, 0.2], kc_range=[0.0, 0.0], na=3, nb=3, nc=1, ) qpoints = RegularKpointGrid( ka_range=[-0.5, 0.5], kb_range=[-0.5, 0.5], kc_range=[0.0, 0.0], na=9, nb=9, nc=1, ) inelastic_transmission_spectrum = InelasticTransmissionSpectrum( configuration=device_configuration, bulk_dynamical_matrix=dynamical_matrix, bulk_hamiltonian_derivatives=hamiltonian_derivatives, energies=numpy.linspace(-0.5, 0.5, 25)*eV, kpoints=kpoints, qpoints=qpoints, self_energy_calculator=RecursionSelfEnergy(), energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, phonon_modes=All, method=XLOE, spectral_representation=True, electrode_extensions=[0, 0], ) nlsave('xloe_V-0.4_bulk.hdf5', inelastic_transmission_spectrum)