# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Two-probe Configuration # ------------------------------------------------------------- # ------------------------------------------------------------- # Left Electrode # ------------------------------------------------------------- # Set up lattice vector_a = [2.88902617589, 0.0, 0.0]*Angstrom vector_b = [0.0, 14.4451308795, 0.0]*Angstrom vector_c = [0.0, 0.0, 4.0857]*Angstrom left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements left_electrode_elements = [Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver] # Define coordinates left_electrode_coordinates = [[ 0. , 0. , 1.021425 ], [ 0. , 2.889026175894, 1.021425 ], [ 0. , 5.778052351788, 1.021425 ], [ 0. , 8.667078527682, 1.021425 ], [ 0. , 11.556104703576, 1.021425 ], [ 1.444513087947, 1.444513087947, 3.064275 ], [ 1.444513087947, 4.333539263841, 3.064275 ], [ 1.444513087947, 7.222565439735, 3.064275 ], [ 1.444513087947, 10.111591615629, 3.064275 ], [ 1.444513087947, 13.000617791522, 3.064275 ]]*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 = [2.88902617589, 0.0, 0.0]*Angstrom vector_b = [0.0, 14.4451308795, 0.0]*Angstrom vector_c = [0.0, 0.0, 7.06373620597]*Angstrom right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates right_electrode_coordinates = [[ 0. , 1.605014542163, 1.177289367661], [ 1.444513087947, 4.012536355408, 1.177289367661], [ 0. , 6.420058168653, 1.177289367661], [ 1.444513087947, 8.827579981898, 1.177289367661], [ 0. , 11.235101795143, 1.177289367661], [ 1.444513087947, 13.642623608388, 1.177289367661], [ 1.444513087947, 0.802507271082, 3.531868102984], [ 0. , 3.210029084327, 3.531868102984], [ 1.444513087947, 5.617550897571, 3.531868102984], [ 0. , 8.025072710816, 3.531868102984], [ 1.444513087947, 10.432594524061, 3.531868102984], [ 0. , 12.840116337306, 3.531868102984], [ 0. , 0. , 5.886446838306], [ 1.444513087947, 2.407521813245, 5.886446838306], [ 0. , 4.81504362649 , 5.886446838306], [ 1.444513087947, 7.222565439735, 5.886446838306], [ 0. , 9.63008725298 , 5.886446838306], [ 1.444513087947, 12.037609066224, 5.886446838306]]*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 = [2.88902617589, 0.0, 0.0]*Angstrom vector_b = [0.0, 14.4451308795, 0.0]*Angstrom vector_c = [0.0, 0.0, 54.9678591915]*Angstrom central_region_lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements central_region_elements = [Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Silver, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold] # Define coordinates central_region_coordinates = [[ 0. , 0. , 1.021425 ], [ 0. , 2.889026175894, 1.021425 ], [ 0. , 5.778052351788, 1.021425 ], [ 0. , 8.667078527682, 1.021425 ], [ 0. , 11.556104703576, 1.021425 ], [ 1.444513087947, 1.444513087947, 3.064275 ], [ 1.444513087947, 4.333539263841, 3.064275 ], [ 1.444513087947, 7.222565439735, 3.064275 ], [ 1.444513087947, 10.111591615629, 3.064275 ], [ 1.444513087947, 13.000617791522, 3.064275 ], [ 0. , 0. , 5.107125 ], [ 0. , 2.889026175894, 5.107125 ], [ 0. , 5.778052351788, 5.107125 ], [ 0. , 8.667078527682, 5.107125 ], [ 0. , 11.556104703576, 5.107125 ], [ 1.444513087947, 1.444513087947, 7.149975 ], [ 1.444513087947, 4.333539263841, 7.149975 ], [ 1.444513087947, 7.222565439735, 7.149975 ], [ 1.444513087947, 10.111591615629, 7.149975 ], [ 1.444513087947, 13.000617791522, 7.149975 ], [ 0. , 0. , 9.192825 ], [ 0. , 2.889026175894, 9.192825 ], [ 0. , 5.778052351788, 9.192825 ], [ 0. , 8.667078527682, 9.192825 ], [ 0. , 11.556104703576, 9.192825 ], [ 1.444513087947, 1.444513087947, 11.235675 ], [ 1.444513087947, 4.333539263841, 11.235675 ], [ 1.444513087947, 7.222565439735, 11.235675 ], [ 1.444513087947, 10.111591615629, 11.235675 ], [ 1.444513087947, 13.000617791522, 11.235675 ], [ 0. , 0. , 13.278525 ], [ 0. , 2.889026175894, 13.278525 ], [ 0. , 5.778052351788, 13.278525 ], [ 0. , 8.667078527682, 13.278525 ], [ 0. , 11.556104703576, 13.278525 ], [ 1.444513087947, 1.444513087947, 15.321375 ], [ 1.444513087947, 4.333539263841, 15.321375 ], [ 1.444513087947, 7.222565439735, 15.321375 ], [ 1.444513087947, 10.111591615629, 15.321375 ], [ 1.444513087947, 13.000617791522, 15.321375 ], [ 0. , 0. , 17.364225 ], [ 0. , 2.889026175894, 17.364225 ], [ 0. , 5.778052351788, 17.364225 ], [ 0. , 8.667078527682, 17.364225 ], [ 0. , 11.556104703576, 17.364225 ], [ 1.444513087947, 1.444513087947, 19.407075 ], [ 1.444513087947, 4.333539263841, 19.407075 ], [ 1.444513087947, 7.222565439735, 19.407075 ], [ 1.444513087947, 10.111591615629, 19.407075 ], [ 1.444513087947, 13.000617791522, 19.407075 ], [ 0. , 0. , 21.449925 ], [ 0. , 2.889026175894, 21.449925 ], [ 0. , 5.778052351788, 21.449925 ], [ 0. , 8.667078527682, 21.449925 ], [ 0. , 11.556104703576, 21.449925 ], [ 1.444513087947, 1.444513087947, 23.492775 ], [ 1.444513087947, 4.333539263841, 23.492775 ], [ 1.444513087947, 7.222565439735, 23.492775 ], [ 1.444513087947, 10.111591615629, 23.492775 ], [ 1.444513087947, 13.000617791522, 23.492775 ], [ 0. , 0. , 25.535625 ], [ 0. , 2.889026175894, 25.535625 ], [ 0. , 8.667078527682, 25.535625 ], [ 0. , 11.556104703576, 25.535625 ], [ 0. , 1.605014542163, 27.890203735323], [ 1.444513087947, 4.012536355408, 27.890203735323], [ 0. , 6.420058168653, 27.890203735323], [ 0. , 11.235101795143, 27.890203735323], [ 1.444513087947, 13.642623608388, 27.890203735323], [ 1.444513087947, 0.802507271082, 30.244782470646], [ 0. , 3.210029084327, 30.244782470646], [ 1.444513087947, 5.617550897571, 30.244782470646], [ 0. , 8.025072710816, 30.244782470646], [ 1.444513087947, 10.432594524061, 30.244782470646], [ 0. , 12.840116337306, 30.244782470646], [ 0. , 0. , 32.599361205968], [ 1.444513087947, 2.407521813245, 32.599361205968], [ 0. , 4.81504362649 , 32.599361205968], [ 1.444513087947, 7.222565439735, 32.599361205968], [ 0. , 9.63008725298 , 32.599361205968], [ 1.444513087947, 12.037609066224, 32.599361205968], [ 0. , 1.605014542163, 34.953939941291], [ 1.444513087947, 4.012536355408, 34.953939941291], [ 0. , 6.420058168653, 34.953939941291], [ 1.444513087947, 8.827579981898, 34.953939941291], [ 0. , 11.235101795143, 34.953939941291], [ 1.444513087947, 13.642623608388, 34.953939941291], [ 1.444513087947, 0.802507271082, 37.308518676613], [ 0. , 3.210029084327, 37.308518676613], [ 1.444513087947, 5.617550897571, 37.308518676613], [ 0. , 8.025072710816, 37.308518676613], [ 1.444513087947, 10.432594524061, 37.308518676613], [ 0. , 12.840116337306, 37.308518676613], [ 0. , 0. , 39.663097411936], [ 1.444513087947, 2.407521813245, 39.663097411936], [ 0. , 4.81504362649 , 39.663097411936], [ 1.444513087947, 7.222565439735, 39.663097411936], [ 0. , 9.63008725298 , 39.663097411936], [ 1.444513087947, 12.037609066224, 39.663097411936], [ 0. , 1.605014542163, 42.017676147259], [ 1.444513087947, 4.012536355408, 42.017676147259], [ 0. , 6.420058168653, 42.017676147259], [ 1.444513087947, 8.827579981898, 42.017676147259], [ 0. , 11.235101795143, 42.017676147259], [ 1.444513087947, 13.642623608388, 42.017676147259], [ 1.444513087947, 0.802507271082, 44.372254882581], [ 0. , 3.210029084327, 44.372254882581], [ 1.444513087947, 5.617550897571, 44.372254882581], [ 0. , 8.025072710816, 44.372254882581], [ 1.444513087947, 10.432594524061, 44.372254882581], [ 0. , 12.840116337306, 44.372254882581], [ 0. , 0. , 46.726833617904], [ 1.444513087947, 2.407521813245, 46.726833617904], [ 0. , 4.81504362649 , 46.726833617904], [ 1.444513087947, 7.222565439735, 46.726833617904], [ 0. , 9.63008725298 , 46.726833617904], [ 1.444513087947, 12.037609066224, 46.726833617904], [ 0. , 1.605014542163, 49.081412353226], [ 1.444513087947, 4.012536355408, 49.081412353226], [ 0. , 6.420058168653, 49.081412353226], [ 1.444513087947, 8.827579981898, 49.081412353226], [ 0. , 11.235101795143, 49.081412353226], [ 1.444513087947, 13.642623608388, 49.081412353226], [ 1.444513087947, 0.802507271082, 51.435991088549], [ 0. , 3.210029084327, 51.435991088549], [ 1.444513087947, 5.617550897571, 51.435991088549], [ 0. , 8.025072710816, 51.435991088549], [ 1.444513087947, 10.432594524061, 51.435991088549], [ 0. , 12.840116337306, 51.435991088549], [ 0. , 0. , 53.790569823872], [ 1.444513087947, 2.407521813245, 53.790569823872], [ 0. , 4.81504362649 , 53.790569823872], [ 1.444513087947, 7.222565439735, 53.790569823872], [ 0. , 9.63008725298 , 53.790569823872], [ 1.444513087947, 12.037609066224, 53.790569823872]]*Angstrom # Set up configuration central_region = BulkConfiguration( bravais_lattice=central_region_lattice, elements=central_region_elements, cartesian_coordinates=central_region_coordinates ) device_configuration = DeviceConfiguration( central_region, [left_electrode, right_electrode], equivalent_electrode_lengths=[8.1714, 7.06373620597]*Angstrom, ) # Add tags device_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, 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]) device_configuration.addTags('Right Interface', [ 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = EAM_Zhou_2004() calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(0.25*Angstrom) device_configuration.setCalculator(calculator) # ------------------------------------------------------------- # Optimize Device Configuration # ------------------------------------------------------------- # Parameters for device configuration optimization. optimize_geometry_parameters = OptimizeGeometryParameters( max_forces=0.05*eV/Angstrom, max_stress=0.1*GPa, max_steps=200, max_step_length=0.2*Angstrom, optimizer_method=LBFGS(), ) optimize_device_configuration = OptimizeDeviceConfiguration( device_configuration=device_configuration, filename=u'Ag100-Au111-default.hdf5', object_id='optimizedeviceconfiguration', optimization_region_length=10.0*Angstrom, optimization_region_center=None, passivate_electrode_surfaces=(True, True), optimize_geometry_parameters=optimize_geometry_parameters, log_filename_prefix='optimizedeviceconfiguration_', ) optimize_device_configuration.update() nlprint(optimize_device_configuration)