# 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, 50.0]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, Oxygen, Lithium, Lithium, Oxygen, Oxygen, Carbon, 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 fractional_coordinates = [[ 0.380624212955, 0. , 0.189439465318], [ 0.762530782053, 0. , 0.212239160329], [ 0.506364858149, 0. , 0.212390556065], [ 0.382559159796, 0. , 0.235559319456], [ 0.004356755633, 0. , 0.243099403578], [ 0.500000107621, 0.500000430093, 0.27312399014 ], [ 0.880624320575, 0.500000430093, 0.281832253384], [ 0.262530674431, 0.500000430093, 0.304631948395], [ 0.006364750527, 0.500000430093, 0.304783344131], [ 0.882559267416, 0.500000430093, 0.327952107522], [ 0.504356863254, 0.500000430093, 0.335492191644], [-0.000000000002, 0. , 0.365516778206], [ 0.380624212953, 0. , 0.37422504145 ], [ 0.762530782051, 0. , 0.397024736461], [ 0.506364858147, 0. , 0.397176132197], [ 0.382559159794, 0. , 0.420344895588], [ 0.004356755631, 0. , 0.42788497971 ], [ 0.500000107619, 0.500000430093, 0.457909566272], [ 0.880624320573, 0.500000430093, 0.466617829516], [ 0.262530674429, 0.500000430093, 0.489417524527], [ 0.006364750525, 0.500000430093, 0.489568920263], [ 0.882559267414, 0.500000430093, 0.512737683654], [ 0.504356863252, 0.500000430093, 0.520277767776], [-0.000000000004, 0. , 0.526302354338], [ 0.333331921577, -0.000000000001, 0.549168707379], [ 0.833332029199, 0.500000430093, 0.549168707379], [ 0.666666822231, -0.000000000001, 0.564833629128], [ 0.166666714609, 0.500000430093, 0.564833629128], [ 0.333331921577, -0.000000000001, 0.580498550875], [ 0.833332029199, 0.500000430093, 0.580498550875], [ 0. , 0. , 0.603364903917], [ 0.500000107622, 0.500000430093, 0.603364903917], [ 0.666668231059, -0.000000000001, 0.626145804208], [ 0.166668123438, 0.500000430093, 0.626145804208], [ 0.333333375715, -0.000000000001, 0.641898174213], [ 0.833333483337, 0.500000430093, 0.641898174213], [ 0.666668231059, -0.000000000001, 0.657650544219], [ 0.166668123438, 0.500000430093, 0.657650544219], [ 0. , 0. , 0.68043144451 ], [ 0.500000107622, 0.500000430093, 0.68043144451 ], [ 0.333331921577, -0.000000000001, 0.703297797551], [ 0.833332029199, 0.500000430093, 0.703297797551], [ 0.666666822231, -0.000000000001, 0.7189627193 ], [ 0.166666714609, 0.500000430093, 0.7189627193 ], [ 0.333331921577, -0.000000000001, 0.734627641047], [ 0.833332029199, 0.500000430093, 0.734627641047], [ 0. , 0. , 0.757493994089], [ 0.500000107622, 0.500000430093, 0.757493994089], [ 0.666668231059, -0.000000000001, 0.78027489438 ], [ 0.166668123438, 0.500000430093, 0.78027489438 ], [ 0.333333375715, -0.000000000001, 0.796027264385], [ 0.833333483337, 0.500000430093, 0.796027264385], [ 0.666668231059, -0.000000000001, 0.811779634391], [ 0.166668123438, 0.500000430093, 0.811779634391], [ 0. , 0. , 0.834560534682], [ 0.500000107622, 0.500000430093, 0.834560534682]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags bulk_configuration.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]) bulk_configuration.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]) bulk_configuration.addTags('li2co3_electrode', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]) bulk_configuration.addTags('li2o2_electrode', [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # Basis Set #---------------------------------------- basis_set = [ GGABasis.Lithium_DoubleZetaPolarized, GGABasis.Carbon_DoubleZetaPolarized, GGABasis.Oxygen_DoubleZetaPolarized, ] #---------------------------------------- # Exchange-Correlation #---------------------------------------- exchange_correlation = GGA.RPBE numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=(9, 15, 1), ) calculator = LCAOCalculator( basis_set=basis_set, exchange_correlation=exchange_correlation, numerical_accuracy_parameters=numerical_accuracy_parameters, ) bulk_configuration.setCalculator(calculator) nlprint(bulk_configuration) bulk_configuration.update() nlsave('interface_bulk_opt.nc', bulk_configuration) # ------------------------------------------------------------- # Optimize Geometry # ------------------------------------------------------------- indices_0 = [40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] constraints = [RigidBody(indices_0), 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] bulk_configuration = OptimizeGeometry( bulk_configuration, max_forces=0.05*eV/Ang, max_steps=200, max_step_length=0.2*Ang, constraints=constraints, trajectory_filename='interface_bulk_opt.nc', disable_stress=True, optimizer_method=LBFGS(), ) nlsave('interface_bulk_opt.nc', bulk_configuration) nlprint(bulk_configuration)