# ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [5.13498, 0.0, 0.0]*Angstrom vector_b = [0.0, -3.45897, 0.0]*Angstrom vector_c = [0.0, 0.0, 9.23927881]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium] # Define coordinates left_electrode_coordinates = [[ 1.95449772104 , 0. , 0.2177065811 ], [ 3.915580315227, 0. , 1.35769133165 ], [ 2.600173419298, 0. , 1.36526111845 ], [ 1.964433634369, 0. , 2.523699288 ], [ 0.02237185304 , 0. , 2.9007034941 ], [ 2.567490552632, -1.729486487679, 4.4019328222 ], [ 4.521988273666, -1.729486487679, 4.8373459844 ], [ 1.34808976259 , -1.729486487679, 5.97733073495 ], [ 0.032682866661, -1.729486487679, 5.98490052175 ], [ 4.531924186996, -1.729486487679, 7.1433386913 ], [ 2.589862405672, -1.729486487679, 7.5203428974 ], [-0.00000000001 , 0. , 9.0215722255 ]]*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('Left Interface') left_electrode.addTags('li2co3_electrode') # ------------------------------------------------------------- # Right Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [5.13498, 0.0, 0.0]*Angstrom vector_b = [0.0, -3.45897, 0.0]*Angstrom vector_c = [0.0, 0.0, 7.70665406]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium] # Define coordinates right_electrode_coordinates = [[ 3.354031312343, 0.00000080576 , 0.569549537625], [ 0.786540759712, -1.729485681922, 0.569549537625], [ 1.642363496849, 0.00000080576 , 1.357168037875], [ 4.209854049486, -1.729485681922, 1.357168037875], [ 3.354031312343, 0.00000080576 , 2.144786538175], [ 0.786540759712, -1.729485681922, 2.144786538175], [-0.06929672078 , 0.000000805757, 3.283831552725], [ 2.498193831857, -1.729485681922, 3.283831552725], [ 3.354031312343, 0.00000080576 , 4.422876567275], [ 0.786540759712, -1.729485681922, 4.422876567275], [ 1.642363496849, 0.00000080576 , 5.210495067525], [ 4.209854049486, -1.729485681922, 5.210495067525], [ 3.354031312343, 0.00000080576 , 5.998113567825], [ 0.786540759712, -1.729485681922, 5.998113567825], [-0.06929672078 , 0.000000805757, 7.137158582375], [ 2.498193831857, -1.729485681922, 7.137158582375]]*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('Right Interface') right_electrode.addTags('li2o2_electrode') # ------------------------------------------------------------- # Central Region # ------------------------------------------------------------- # Set up lattice vector_a = [5.13498, 0.0, 0.0]*Angstrom vector_b = [0.0, -3.45897, 0.0]*Angstrom vector_c = [0.0, 0.0, 36.9510044716]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Carbon, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Lithium, Lithium] # Define coordinates central_region_coordinates = [[ 1.95449772104 , 0. , 0.2177065811 ], [ 3.915580315227, 0. , 1.35769133165 ], [ 2.600173419298, 0. , 1.36526111845 ], [ 1.964433634369, 0. , 2.523699288 ], [ 0.02237185304 , 0. , 2.9007034941 ], [ 2.567490552632, -1.729486487679, 4.4019328222 ], [ 4.521988273666, -1.729486487679, 4.8373459844 ], [ 1.34808976259 , -1.729486487679, 5.97733073495 ], [ 0.032682866661, -1.729486487679, 5.98490052175 ], [ 4.531924186996, -1.729486487679, 7.1433386913 ], [ 2.589862405672, -1.729486487679, 7.5203428974 ], [ -0.00000000001 , 0. , 9.0215722255 ], [ 1.954497721029, 0. , 9.4569853877 ], [ 3.945314545152, -0.000000113638, 10.52710295575 ], [ 2.640452127956, -0.000000093129, 10.5606693969 ], [ 2.039468692835, -0.000000167525, 11.74539501775 ], [ 0.003190182949, -0.000000167214, 12.1112079491 ], [ 2.542133175927, -1.72948515042 , 13.0038880872 ], [ 4.663415583007, -1.729485096156, 13.37961883405 ], [ 0.070262755592, -1.729485180883, 14.5760847716 ], [ 1.362853481672, -1.729485081943, 14.719331755 ], [ 4.444143531112, -1.729485349781, 15.6544338432 ], [ 2.546018422478, -1.729485368048, 16.40394858635 ], [ -0.129192281474, -0.000000581259, 16.8792506737 ], [ 1.606971761567, -0.000000122306, 17.846172999 ], [ 4.174697325883, -1.729485031774, 18.156685102 ], [ 0.876797539826, -1.729485158787, 18.7354601751 ], [ 3.358267279039, -0.000000024427, 18.79070052455 ], [ 1.589137522931, -0.000000119781, 19.4293944483 ], [ 4.200439413184, -1.729485000014, 19.7234065001 ], [ -0.049898134669, -0.00000010307 , 20.7109546466 ], [ 2.602557257087, -1.72948498651 , 20.88016266925 ], [ 0.965044406537, -1.72948508818 , 22.05284837795 ], [ 3.516669946255, -0.0000001951 , 22.05690063695 ], [ 4.319439809132, -1.7294851772 , 22.8056975305 ], [ 1.718116545687, -0.000000100026, 22.8104581491 ], [ 0.946891217389, -1.729485120348, 23.6274824219 ], [ 3.504359114494, -0.000000160216, 23.6306694038 ], [ 2.58671840814 , -1.729485146252, 24.7605492418 ], [ 0.010617943828, -0.000000097166, 24.77348971925 ], [ 1.642356029879, 0.00000080576 , 25.9650451078 ], [ 4.209846582516, -1.729485681922, 25.9650451078 ], [ 3.35402407804 , 0.00000080576 , 26.74829119525 ], [ 0.786533525403, -1.729485681922, 26.74829119525 ], [ 1.642356029879, 0.00000080576 , 27.5315372826 ], [ 4.209846582516, -1.729485681922, 27.5315372826 ], [ -0.06929672078 , 0.000000805757, 28.6748549347 ], [ 2.498193831857, -1.729485681922, 28.6748549347 ], [ 3.354031312343, 0.00000080576 , 29.81389994925 ], [ 0.786540759712, -1.729485681922, 29.81389994925 ], [ 1.642363496849, 0.00000080576 , 30.6015184495 ], [ 4.209854049486, -1.729485681922, 30.6015184495 ], [ 3.354031312343, 0.00000080576 , 31.3891369498 ], [ 0.786540759712, -1.729485681922, 31.3891369498 ], [ -0.06929672078 , 0.000000805757, 32.52818196435 ], [ 2.498193831857, -1.729485681922, 32.52818196435 ], [ 3.354031312343, 0.00000080576 , 33.6672269789 ], [ 0.786540759712, -1.729485681922, 33.6672269789 ], [ 1.642363496849, 0.00000080576 , 34.45484547915 ], [ 4.209854049486, -1.729485681922, 34.45484547915 ], [ 3.354031312343, 0.00000080576 , 35.24246397945 ], [ 0.786540759712, -1.729485681922, 35.24246397945 ], [ -0.06929672078 , 0.000000805757, 36.381508994 ], [ 2.498193831857, -1.729485681922, 36.381508994 ]]*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('Left Interface', [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) central_region.addTags('Right Interface', [24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) central_region.addTags('li2co3_electrode', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]) central_region.addTags('li2o2_electrode', [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode] ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = [ GGABasis.Lithium_DoubleZetaPolarized, GGABasis.Carbon_DoubleZetaPolarized, GGABasis.Oxygen_DoubleZetaPolarized, ] #---------------------------------------- # Exchange-Correlation #---------------------------------------- exchange_correlation = GGA.RPBE #---------------------------------------- # Numerical Accuracy Settings #---------------------------------------- left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=(7, 15, 200), ) right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=(7, 15, 200), ) device_numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=(7, 15, 200), ) #---------------------------------------- # 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) nlprint(device_configuration) device_configuration.update() nlsave('device_interface.nc', device_configuration) # ------------------------------------------------------------- # Transmission Spectrum # ------------------------------------------------------------- transmission_spectrum = TransmissionSpectrum( configuration=device_configuration, energies=numpy.linspace(-3,3,201)*eV, kpoints=MonkhorstPackGrid(13,21), energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, self_energy_calculator=RecursionSelfEnergy(), ) nlsave('device_interface.nc', transmission_spectrum) nlprint(transmission_spectrum) # ------------------------------------------------------------- # Projected Local Density Of States # ------------------------------------------------------------- projected_local_density_of_states = ProjectedLocalDensityOfStates( configuration=device_configuration, method=DeviceDensityOfStates, energies=numpy.linspace(-4, 4, 301)*eV, kpoints=MonkhorstPackGrid(13, 21), contributions=All, self_energy_calculator=RecursionSelfEnergy(), energy_zero_parameter=AverageFermiLevel, infinitesimal=1e-06*eV, ) nlsave('device_interface.nc', projected_local_density_of_states)