# ------------------------------------------------------------- # Nudged Elastic Band Configuration # ------------------------------------------------------------- # Setup the configuration list configuration_list = [] # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.988472839537, 0.380487954543, 0.219403356388], [ 0.489699842761, 0.380052398128, 0.214466715534], [ 0.988483902113, 0.879986001237, 0.219439062887], [ 0.489484192973, 0.880361864144, 0.214511356832], [ 0.731841640524, 0.396553093461, 0.273542895729], [ 0.247034655423, 0.366341172793, 0.272629406254], [ 0.731783549478, 0.863993844702, 0.273548570205], [ 0.246899360416, 0.894633998844, 0.272764646715], [ 0.612616842921, 0.130322809391, 0.301314064193], [ 0.319288360892, 0.13065109226 , 0.330803053002], [ 0.661170499768, 0.630281650803, 0.333204201241], [ 0.359318245222, 0.63044940258 , 0.306351835717], [ 0.194216406433, 0.625283317927, 0.435942868221], [ 0.362215060971, 0.609965908055, 0.465291230121], [ 0.239339409362, 0.629868925844, 0.376131803842], [ 0.079936050243, 0.470692973992, 0.444518200247], [ 0.102396316136, 0.791723303744, 0.448077120962]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.989050030769, 0.380409021922, 0.21937777858 ], [ 0.489127015189, 0.379853357616, 0.214401874625], [ 0.989072127383, 0.880058669093, 0.219412223677], [ 0.488951196951, 0.880559941983, 0.21443585603 ], [ 0.731878330384, 0.394678914212, 0.273226875103], [ 0.247323988048, 0.368052856336, 0.272723866337], [ 0.731829537204, 0.865808918801, 0.273233828702], [ 0.247234388092, 0.892894627664, 0.272838195947], [ 0.611457130135, 0.130293215826, 0.301752564457], [ 0.317888992543, 0.13061146385 , 0.330215109548], [ 0.656856008142, 0.630245528955, 0.331109663077], [ 0.352456360788, 0.630436593487, 0.309117326033], [ 0.304734302934, 0.625966142403, 0.430848402568], [ 0.478161256357, 0.613629901491, 0.454292797478], [ 0.243274754445, 0.629996646672, 0.376225459543], [ 0.20056868228 , 0.470335643059, 0.443345348157], [ 0.218546721611, 0.790860181745, 0.44630009351 ]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.989627222001, 0.380330089302, 0.219352200773], [ 0.488554187616, 0.379654317103, 0.214337033715], [ 0.989660352652, 0.880131336948, 0.219385384467], [ 0.48841820093 , 0.880758019823, 0.214360355228], [ 0.731915020243, 0.392804734964, 0.272910854476], [ 0.247613320673, 0.36976453988 , 0.27281832642 ], [ 0.73187552493 , 0.867623992901, 0.272919087198], [ 0.247569415767, 0.891155256483, 0.272911745179], [ 0.610297417348, 0.130263622261, 0.302191064721], [ 0.316489624195, 0.13057183544 , 0.329627166093], [ 0.652541516516, 0.630209407107, 0.329015124913], [ 0.345594476354, 0.630423784393, 0.31188281635 ], [ 0.415252199435, 0.626648966878, 0.425753936916], [ 0.594107451743, 0.617293894927, 0.443294364836], [ 0.247210099528, 0.6301243675 , 0.376319115245], [ 0.321201314317, 0.469978312125, 0.442172496067], [ 0.334697127087, 0.789997059745, 0.444523066058]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.990204413232, 0.380251156681, 0.219326622965], [ 0.487981360044, 0.37945527659 , 0.214272192806], [ 0.990248577922, 0.880204004804, 0.219358545257], [ 0.487885204908, 0.880956097662, 0.214284854427], [ 0.731951710103, 0.390930555715, 0.27259483385 ], [ 0.247902653298, 0.371476223423, 0.272912786503], [ 0.731921512656, 0.869439067 , 0.272604345695], [ 0.247904443443, 0.889415885303, 0.272985294412], [ 0.609137704562, 0.130234028696, 0.302629564986], [ 0.315090255847, 0.13053220703 , 0.329039222639], [ 0.648227024891, 0.630173285259, 0.326920586748], [ 0.338732591919, 0.6304109753 , 0.314648306666], [ 0.525770095936, 0.627331791354, 0.420659471263], [ 0.710053647129, 0.620957888364, 0.432295932193], [ 0.251145444611, 0.630252088329, 0.376412770946], [ 0.441833946354, 0.469620981192, 0.440999643976], [ 0.450847532562, 0.789133937745, 0.442746038606]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.990781604464, 0.38017222406 , 0.219301045157], [ 0.487408532472, 0.379256236078, 0.214207351896], [ 0.990836803192, 0.88027667266 , 0.219331706047], [ 0.487352208887, 0.881154175501, 0.214209353625], [ 0.731988399963, 0.389056376467, 0.272278813223], [ 0.248191985924, 0.373187906966, 0.273007246585], [ 0.731967500381, 0.8712541411 , 0.272289604191], [ 0.248239471119, 0.887676514123, 0.273058843644], [ 0.607977991776, 0.13020443513 , 0.30306806525 ], [ 0.313690887498, 0.13049257862 , 0.328451279185], [ 0.643912533265, 0.630137163411, 0.324826048584], [ 0.331870707485, 0.630398166206, 0.317413796982], [ 0.636287992437, 0.628014615829, 0.41556500561 ], [ 0.825999842516, 0.6246218818 , 0.421297499551], [ 0.255080789695, 0.630379809157, 0.376506426647], [ 0.562466578391, 0.469263650259, 0.439826791886], [ 0.566997938038, 0.788270815746, 0.440969011154]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [7.680028171823331, 0.0, 0.0]*Angstrom vector_b = [0.0, 7.680028171823331, 0.0]*Angstrom vector_c = [0.0, 0.0, 25.1459]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements 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, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates fractional_coordinates = [[ 0.739584288592, 0.380207855704, 0.053990909055], [ 0.239584288592, 0.380207855704, 0.053990909055], [ 0.739584288592, 0.880207855704, 0.053990909055], [ 0.239584288592, 0.880207855704, 0.053990909055], [ 0.739584288592, 0.130207855704, 0.10798181811 ], [ 0.239584288592, 0.130207855704, 0.10798181811 ], [ 0.739584288592, 0.630207855704, 0.10798181811 ], [ 0.239584288592, 0.630207855704, 0.10798181811 ], [ 0.989584288592, 0.130207855704, 0.161972727165], [ 0.489584288592, 0.130207855704, 0.161972727165], [ 0.989584288592, 0.630207855704, 0.161972727165], [ 0.489584288592, 0.630207855704, 0.161972727165], [ 0.991358795696, 0.380093291439, 0.21927546735 ], [ 0.4868357049 , 0.379057195565, 0.214142510987], [ 0.991425028461, 0.880349340515, 0.219304866837], [ 0.486819212865, 0.881352253341, 0.214133852823], [ 0.732025089823, 0.387182197218, 0.271962792597], [ 0.248481318549, 0.374899590509, 0.273101706668], [ 0.732013488107, 0.873069215199, 0.271974862688], [ 0.248574498794, 0.885937142942, 0.273132392876], [ 0.606818278989, 0.130174841565, 0.303506565514], [ 0.31229151915 , 0.13045295021 , 0.32786333573 ], [ 0.639598041639, 0.630101041563, 0.32273151042 ], [ 0.325008823051, 0.630385357112, 0.320179287298], [ 0.746805888938, 0.628697440305, 0.410470539957], [ 0.941946037902, 0.628285875236, 0.410299066908], [ 0.259016134778, 0.630507529985, 0.376600082349], [ 0.683099210428, 0.468906319325, 0.438653939796], [ 0.683148343513, 0.787407693746, 0.439191983702]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags configuration.addTags('H_Si', [25, 26, 27, 28]) configuration.addTags('Selection 0', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) configuration.addTags('constrained', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]) # Append to the list of configurations configuration_list.append(configuration) # Construct the Nudged Elastic Band object neb_configuration = NudgedElasticBand( configuration_list, generate_images=False) # Unreference the temporary configuration variable del configuration # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- #---------------------------------------- # PAW Data Set #---------------------------------------- basis_set = [ PAWPBESuggested.Silicon, PAWPBESuggested.Hydrogen, ] #---------------------------------------- # Exchange-Correlation #---------------------------------------- exchange_correlation = GGA.PBE density_mesh_cutoff = OptimizedFFTGridSampling( energy_cutoff=1520.0*eV, maximum_average_prime_factor=5.0, maximum_grid_enlargement=0.1, ) k_point_sampling = MonkhorstPackGrid( na=6, nb=6, nc=1, symmetries=[ ([[ 1., 0., 0.], [ 0., 1., 0.], [ 0., 0., 1.]], [ 0., 0., 0.]), ([[-1., 0., 0.], [ 0.,-1., 0.], [ 0., 0.,-1.]], [ 0., 0., 0.]), ], force_timereversal=True, shift_to_gamma=[True, True, True], ) exx_grid_cutoff = OptimizedFFTGridSampling( energy_cutoff=760.0*eV, maximum_average_prime_factor=5.0, maximum_grid_enlargement=0.1, ) exact_exchange_parameters = ExactExchangeParameters( aux_basis_tolerance=0.001, number_of_waves=1024, maximum_wave_vector=50.0, integral_tolerance=0.0001, relative_screening_tolerance=0.01, ) compensation_charge_mesh_cutoff = OptimizedFFTGridSampling( energy_cutoff=1520.0*eV, maximum_average_prime_factor=5.0, maximum_grid_enlargement=0.1, ) numerical_accuracy_parameters = NumericalAccuracyParameters( density_mesh_cutoff=density_mesh_cutoff, k_point_sampling=k_point_sampling, radial_step_size=0.001*Bohr, density_cutoff=1e-06, interaction_max_range=20.0*Angstrom, number_of_reciprocal_points=1024, reciprocal_energy_cutoff=1250.0*Hartree, bands_per_electron=1.2, occupation_method=GaussianSmearing(1000.0*Kelvin*boltzmann_constant), exx_grid_cutoff=exx_grid_cutoff, exact_exchange_parameters=exact_exchange_parameters, compensation_charge_mesh_cutoff=compensation_charge_mesh_cutoff, ) iteration_control_parameters = IterationControlParameters( tolerance=0.0001, max_steps=100, algorithm=PulayMixer(), damping_factor=0.2, number_of_history_steps=5, start_mixing_after_step=0, mixing_variable=HamiltonianVariable, preconditioner=Preconditioner.Off, linear_dependence_threshold=0.0, max_exx_updates=50, non_convergence_behavior=ContinueCalculation(), enable_scf_stop_file=True, ) poisson_solver = FastFourierSolver() initialization_method = BasisSetInitialization() density_matrix_method = PPCGSolver( absolute_tolerance=1e-08, relative_tolerance=1e-99, maximum_number_of_iterations=2, block_size=5, rr_period=3, buffer_states=0.05, initialization_method=initialization_method, ) algorithm_parameters = AlgorithmParameters( density_matrix_method=density_matrix_method, store_grids=True, store_basis_on_grid=Automatic, store_energy_density_matrix=Automatic, scf_restart_step_length=0.1*Angstrom, use_symmetries=Automatic, ) parallel_parameters = ParallelParameters( processes_per_neb_image=None, processes_per_individual=None, processes_per_bias_point=None, processes_per_saddle_search=1, ) checkpoint_handler = CheckpointHandler( time_interval=0.5*Hour, ) calculator = PlaneWaveCalculator( wave_function_cutoff=380.0*eV, basis_set=basis_set, exchange_correlation=exchange_correlation, numerical_accuracy_parameters=numerical_accuracy_parameters, iteration_control_parameters=iteration_control_parameters, poisson_solver=poisson_solver, algorithm_parameters=algorithm_parameters, parallel_parameters=parallel_parameters, checkpoint_handler=checkpoint_handler, charge=0.0, correction_extension=None, fixed_spin_moment=False, store_wave_functions=False, processes_per_kpoint=Automatic, ) neb_configuration.setCalculator(calculator) neb_configuration.update() nlsave('NEB-a-b.hdf5', neb_configuration) # ------------------------------------------------------------- # Optimize Geometry # ------------------------------------------------------------- constraints = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] neb_configuration = OptimizeNudgedElasticBand( neb_configuration, max_forces=0.02*eV/Ang, max_steps=200, max_step_length=0.2*Ang, constraints=constraints, trajectory_filename='NEB-a-b.hdf5', trajectory_interval=5, restart_strategy=NoRestart, optimizer_method=LBFGS(), preoptimization=False, climbing_image=True, ) nlsave('NEB-a-b.hdf5', neb_configuration) nlprint(neb_configuration)