# Set minimal log verbosity setVerbosity(MinimalLog) from QATK.Analysis import * from QATK.Calculators.DFT import * from QATK.Core import * # %% Device: Copper # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [3.61496, 0.0, 0.0]*Angstrom vector_b = [0.0, 20.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 3.61496]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper] # Define coordinates left_electrode_coordinates = [[ 2.71122, 5.4813 , 0.9038 ], [ 0.90374, 7.28878, 0.9038 ], [ 2.71122, 9.09626, 0.9038 ], [ 0.90374, 10.90374, 0.9038 ], [ 2.71122, 12.71122, 0.9038 ], [ 0.90374, 14.5187 , 0.9038 ], [ 0.90374, 5.4813 , 2.71128], [ 2.71122, 7.28878, 2.71128], [ 0.90374, 9.09626, 2.71128], [ 2.71122, 10.90374, 2.71128], [ 0.90374, 12.71122, 2.71128], [ 2.71122, 14.5187 , 2.71128]]*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 = [3.61496, 0.0, 0.0]*Angstrom vector_b = [0.0, 20.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 3.61496]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper] # Define coordinates right_electrode_coordinates = [[ 0.90374, 5.4813 , 0.90374], [ 2.71122, 7.28878, 0.90374], [ 0.90374, 9.09626, 0.90374], [ 2.71122, 10.90374, 0.90374], [ 0.90374, 12.71122, 0.90374], [ 2.71122, 14.5187 , 0.90374], [ 2.71122, 5.4813 , 2.71122], [ 0.90374, 7.28878, 2.71122], [ 2.71122, 9.09626, 2.71122], [ 0.90374, 10.90374, 2.71122], [ 2.71122, 12.71122, 2.71122], [ 0.90374, 14.5187 , 2.71122]]*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 = [7.22992, 0.0, 0.0]*Angstrom vector_b = [0.0, 20.0, 0.0]*Angstrom vector_c = [0.0, 0.0, 41.57209999999999]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper] # Define coordinates central_region_coordinates = [[ 2.71122 , 5.4813 , 0.9038 ], [ 0.90374 , 7.28878 , 0.9038 ], [ 2.71122 , 9.09626 , 0.9038 ], [ 0.90374 , 10.90374 , 0.9038 ], [ 2.71122 , 12.71122 , 0.9038 ], [ 0.90374 , 14.5187 , 0.9038 ], [ 0.90374 , 5.4813 , 2.71128 ], [ 2.71122 , 7.28878 , 2.71128 ], [ 0.90374 , 9.09626 , 2.71128 ], [ 2.71122 , 10.90374 , 2.71128 ], [ 0.90374 , 12.71122 , 2.71128 ], [ 2.71122 , 14.5187 , 2.71128 ], [ 2.71122 , 5.4813 , 4.51876 ], [ 0.90374 , 7.28878 , 4.51876 ], [ 2.71122 , 9.09626 , 4.51876 ], [ 0.90374 , 10.90374 , 4.51876 ], [ 2.71122 , 12.71122 , 4.51876 ], [ 0.90374 , 14.5187 , 4.51876 ], [ 0.90374 , 5.4813 , 6.32624 ], [ 2.71122 , 7.28878 , 6.32624 ], [ 0.90374 , 9.09626 , 6.32624 ], [ 2.71122 , 10.90374 , 6.32624 ], [ 0.90374 , 12.71122 , 6.32624 ], [ 2.71122 , 14.5187 , 6.32624 ], [ 2.71122 , 5.4813 , 8.13372 ], [ 0.90374 , 7.28878 , 8.13372 ], [ 2.71122 , 9.09626 , 8.13372 ], [ 0.90374 , 10.90374 , 8.13372 ], [ 2.71122 , 12.71122 , 8.13372 ], [ 0.90374 , 14.5187 , 8.13372 ], [ 0.90374 , 5.4813 , 9.9412 ], [ 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13.554712134973], [ 2.691321638043, 7.31864419073 , 13.54040326489 ], [ 6.345950918599, 7.316882075448, 13.539844214127], [ 0.901591192811, 9.110310404279, 13.537901823189], [ 4.52043557002 , 9.103038007289, 13.538077479783], [ 2.712578625225, 10.892606054625, 13.539952789266], [ 6.324652573286, 10.898358802915, 13.541449195404], [ 0.923880886385, 12.686689971706, 13.546840884428], [ 4.498563056852, 12.686021487975, 13.546742135722], [ 6.326270534336, 14.4021003298 , 13.55818815168 ], [ 2.732238086074, 5.615845738837, 15.369863021378], [ 6.302696547979, 5.614789223105, 15.383403736134], [ 0.900436976665, 7.323929662436, 15.344039811387], [ 4.521151431516, 7.350486429535, 15.353321364283], [ 2.705533300059, 9.104564852453, 15.347131562072], [ 6.331502042648, 9.107458775631, 15.349966064541], [ 0.908350516239, 10.892961048605, 15.349496535155], [ 4.513949754681, 10.885843791636, 15.348493263227], [ 2.712370853045, 12.682774060526, 15.349001827924], [ 6.3249168393 , 12.65554374204 , 15.356876244876], [ 0.879884773873, 14.395598728279, 15.386206747743], [ 4.542470399592, 14.396966343596, 15.386285408254], [ 0.926662709271, 5.615709553509, 17.149155140008], [ 4.498419932927, 5.615463384698, 17.163064151919], [ 2.710209015391, 7.350408326515, 17.173397538782], [ 6.328151738505, 7.326141139845, 17.183971855507], [ 0.899461721337, 9.103461526884, 17.164384505766], [ 4.523267521952, 9.107673534556, 17.168074423555], [ 2.710374363361, 10.877773897081, 17.158373283478], [ 6.327229158425, 10.88069573193 , 17.160330176113], [ 0.906555569656, 12.656196684712, 17.168758544591], [ 4.515889905983, 12.654281477898, 17.167727707765], [ 2.711620298255, 14.408579734934, 17.170235735932], [ 6.325765541612, 14.4071946295 , 17.18481509348 ], [ 2.710615922996, 5.606257149312, 18.983127575446], [ 0.886894051055, 7.323556234558, 18.983071649976], [ 4.535557968239, 7.326099916725, 18.982870911513], [ 2.710921164062, 9.107945974885, 18.978354646618], [ 6.32685846104 , 9.111729136128, 18.97924558238 ], [ 0.905600606407, 10.878485151123, 18.972797610116], [ 4.517005118559, 10.879641296797, 18.973971768096], [ 2.711202549918, 12.650829390236, 18.969242592329], [ 6.326247032835, 12.64917258471 , 18.96911103245 ], [ 0.905130992026, 14.40655813822 , 18.97373511486 ], [ 4.51729915755 , 14.40548288744 , 18.973034701604], [ 0.925364044057, 5.607373472859, 20.808058638915], [ 4.497128551777, 5.607658049756, 20.807473482265], [ 2.711225260396, 7.351503954298, 20.785166170507], [ 6.326437752644, 7.32067872483 , 20.772502131563], [ 0.897858878901, 9.112788771164, 20.788821464972], [ 4.524822892257, 9.113224916202, 20.788683282761], [ 2.711170443813, 10.881526350094, 20.791386628179], [ 6.32634936754 , 10.887432169782, 20.794154043682], [ 0.904992201369, 12.643719625744, 20.77486532059 ], [ 4.51746048337 , 12.644104376454, 20.775310610141], [ 2.711167818461, 14.39450734178 , 20.763345132206], [ 6.326227764974, 14.393541806374, 20.761493483573], [ 2.71132244127 , 5.601467209012, 22.593383011079], [ 6.326249922295, 5.601258929406, 22.594083137833], [ 0.900138804767, 7.348344886915, 22.594825507259], [ 4.522472279182, 7.348397765573, 22.594932868172], [ 2.711400733096, 9.119964549882, 22.600730031545], [ 6.326130992594, 9.111390729738, 22.600305974239], [ 0.901755591863, 10.899978406428, 22.608598517296], [ 4.520708059932, 10.899811306932, 22.608319209637], [ 2.711172271104, 12.672955206313, 22.605809624417], [ 6.32622199181 , 12.677754176655, 22.607147357599], [ 0.90495199059 , 14.373449285203, 22.523787346349], [ 4.51748032424 , 14.373800554092, 22.524142064843], [ 0.92610524021 , 5.607155478048, 24.379828597235], [ 4.496414218725, 5.607088503741, 24.379917981007], [ 2.711245539868, 7.347722648673, 24.407569433128], [ 6.32621513221 , 7.317728380278, 24.419556979142], [ 0.897593182964, 9.107742011807, 24.410932487151], [ 4.524857297408, 9.107744506444, 24.411048204016], [ 2.711230752699, 10.89747405247 , 24.405940137081], [ 6.326161240229, 10.903177674802, 24.40351076817 ], [ 0.90518108748 , 12.710823500579, 24.401499584608], [ 4.517250330975, 12.710739316593, 24.401443911675], [ 2.711217177146, 5.602351010412, 26.210519080485], [ 0.885574576108, 7.316661442286, 26.21396592268 ], [ 4.536878735483, 7.316640317322, 26.213932509411], [ 2.711185015239, 9.109932750912, 26.211735202222], [ 6.326207509122, 9.115034983517, 26.212559033311], [ 0.904907717955, 10.905078957194, 26.202413023462], [ 4.517525078255, 10.905108451922, 26.202491610756], [ 2.711212693934, 12.677243947774, 26.199866471461], [ 6.326179508169, 12.677596176934, 26.19932323978 ], [ 0.903540061726, 14.37283511275 , 26.280693398991], [ 4.518892459966, 14.372800970456, 26.280650793327], [ 0.928204354338, 5.599412530424, 28.040228424803], [ 4.494232556037, 5.599418509661, 28.040221327671], [ 2.711227162194, 7.342709113004, 28.023003615925], [ 6.326167660671, 7.313968009597, 28.012972117014], [ 0.898087180911, 9.10936110607 , 28.017338785912], [ 4.524346305531, 9.109343561732, 28.017302209121], [ 2.7112068087 , 10.883424772229, 28.021446704341], [ 6.326185789386, 10.890833089282, 28.022681459954], [ 0.905112937141, 12.649660216445, 28.038211469106], [ 4.517319823636, 12.649680620902, 28.03823983553 ], [ 2.711218752007, 14.399632398157, 28.038610732645], [ 6.326173942167, 14.397862380544, 28.038241289531], [ 2.711217391097, 5.563976266202, 29.832439555584], [ 6.326177787799, 5.565183507852, 29.818886265202], [ 0.901824895892, 7.31660833086 , 29.840635592654], [ 4.520609687996, 7.316609554761, 29.840637539824], [ 2.711219361011, 9.106055993224, 29.834524889035], [ 6.32617484593 , 9.101788926321, 29.830758306792], [ 0.90264015831 , 10.886149960163, 29.837941934345], [ 4.519794176983, 10.886145600444, 29.837935238076], [ 2.711215908113, 12.680641594093, 29.849502431238], [ 6.326178478292, 12.682649566487, 29.850472457453], [ 0.904129082017, 14.437985449515, 29.826158713677], [ 4.518305195137, 14.43798814069 , 29.826162523896], [ 0.90374 , 5.4813 , 31.63096 ], [ 2.71122 , 7.28878 , 31.63096 ], [ 0.90374 , 9.09626 , 31.63096 ], [ 2.71122 , 10.90374 , 31.63096 ], [ 0.90374 , 12.71122 , 31.63096 ], [ 2.71122 , 14.5187 , 31.63096 ], [ 2.71122 , 5.4813 , 33.43844 ], [ 0.90374 , 7.28878 , 33.43844 ], [ 2.71122 , 9.09626 , 33.43844 ], [ 0.90374 , 10.90374 , 33.43844 ], [ 2.71122 , 12.71122 , 33.43844 ], [ 0.90374 , 14.5187 , 33.43844 ], [ 0.90374 , 5.4813 , 35.24592 ], [ 2.71122 , 7.28878 , 35.24592 ], [ 0.90374 , 9.09626 , 35.24592 ], [ 2.71122 , 10.90374 , 35.24592 ], [ 0.90374 , 12.71122 , 35.24592 ], [ 2.71122 , 14.5187 , 35.24592 ], [ 2.71122 , 5.4813 , 37.0534 ], [ 0.90374 , 7.28878 , 37.0534 ], [ 2.71122 , 9.09626 , 37.0534 ], [ 0.90374 , 10.90374 , 37.0534 ], [ 2.71122 , 12.71122 , 37.0534 ], [ 0.90374 , 14.5187 , 37.0534 ], [ 0.90374 , 5.4813 , 38.86088 ], [ 2.71122 , 7.28878 , 38.86088 ], [ 0.90374 , 9.09626 , 38.86088 ], [ 2.71122 , 10.90374 , 38.86088 ], [ 0.90374 , 12.71122 , 38.86088 ], [ 2.71122 , 14.5187 , 38.86088 ], [ 2.71122 , 5.4813 , 40.66836 ], [ 0.90374 , 7.28878 , 40.66836 ], [ 2.71122 , 9.09626 , 40.66836 ], [ 0.90374 , 10.90374 , 40.66836 ], [ 2.71122 , 12.71122 , 40.66836 ], [ 0.90374 , 14.5187 , 40.66836 ], [ 4.5187 , 5.4813 , 31.63096 ], [ 6.32618 , 7.28878 , 31.63096 ], [ 4.5187 , 9.09626 , 31.63096 ], [ 6.32618 , 10.90374 , 31.63096 ], [ 4.5187 , 12.71122 , 31.63096 ], [ 6.32618 , 14.5187 , 31.63096 ], [ 6.32618 , 5.4813 , 33.43844 ], [ 4.5187 , 7.28878 , 33.43844 ], [ 6.32618 , 9.09626 , 33.43844 ], [ 4.5187 , 10.90374 , 33.43844 ], [ 6.32618 , 12.71122 , 33.43844 ], [ 4.5187 , 14.5187 , 33.43844 ], [ 4.5187 , 5.4813 , 35.24592 ], [ 6.32618 , 7.28878 , 35.24592 ], [ 4.5187 , 9.09626 , 35.24592 ], [ 6.32618 , 10.90374 , 35.24592 ], [ 4.5187 , 12.71122 , 35.24592 ], [ 6.32618 , 14.5187 , 35.24592 ], [ 6.32618 , 5.4813 , 37.0534 ], [ 4.5187 , 7.28878 , 37.0534 ], [ 6.32618 , 9.09626 , 37.0534 ], [ 4.5187 , 10.90374 , 37.0534 ], [ 6.32618 , 12.71122 , 37.0534 ], [ 4.5187 , 14.5187 , 37.0534 ], [ 4.5187 , 5.4813 , 38.86088 ], [ 6.32618 , 7.28878 , 38.86088 ], [ 4.5187 , 9.09626 , 38.86088 ], [ 6.32618 , 10.90374 , 38.86088 ], [ 4.5187 , 12.71122 , 38.86088 ], [ 6.32618 , 14.5187 , 38.86088 ], [ 6.32618 , 5.4813 , 40.66836 ], [ 4.5187 , 7.28878 , 40.66836 ], [ 6.32618 , 9.09626 , 40.66836 ], [ 4.5187 , 10.90374 , 40.66836 ], [ 6.32618 , 12.71122 , 40.66836 ], [ 4.5187 , 14.5187 , 40.66836 ]]*Angstrom # Set up configuration central_region = BulkConfiguration( bravais_lattice=central_region_lattice, elements=central_region_elements, cartesian_coordinates=central_region_coordinates ) device_copper = DeviceConfiguration( central_region, [left_electrode, right_electrode], equivalent_electrode_lengths=[10.84488, 10.84488]*Angstrom, transverse_electrode_repetitions=[[2, 1], [2, 1]], ) device_copper_name = "Device: Copper" # %% Set DeviceLCAOCalculator # %% DeviceLCAOCalculator k_point_sampling = KpointDensity( density_a=4.0 * Angstrom, density_b=4.0 * Angstrom, density_c=150.0 * Angstrom ) numerical_accuracy_parameters = NumericalAccuracyParameters( k_point_sampling=k_point_sampling ) model = PretrainedGridValuesModels.effective_potential_Cu grid_values_predictor = EffectivePotentialPredictor( model=model, ) device_algorithm_parameters = DeviceAlgorithmParameters( grid_values_predictor=grid_values_predictor ) calculator = DeviceLCAOCalculator( numerical_accuracy_parameters=numerical_accuracy_parameters, iteration_control_parameters=NonSelfconsistent, device_algorithm_parameters=device_algorithm_parameters, checkpoint_handler=NoCheckpointHandler, ) # %% Set Calculator device_copper.setCalculator(calculator) device_copper.update() nlsave('Device_Copper_ML_non-SCF.hdf5', device_copper) # %% TransmissionSpectrum kpoints = MonkhorstPackGrid(na=21, nb=1, nc=1) transmission_spectrum = TransmissionSpectrum( configuration=device_copper, energies=numpy.linspace(-0.1, 0.1, 11) * eV, kpoints=kpoints, ) nlsave( 'Device_Copper_ML_non-SCF.hdf5', transmission_spectrum, object_id='Transmission SCF' )