# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [16.646425, 0.0, 0.0]*Angstrom vector_b = [-8.32321249999, 14.4162269322, 0.0]*Angstrom vector_c = [0.0, 0.0, 21.326457581]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum] # Define coordinates fractional_coordinates = [[ 0.055555555556, 0.111111111111, 0.10621977455 ], [ 0.222222222222, 0.111111111111, 0.10621977455 ], [ 0.388888888889, 0.111111111111, 0.10621977455 ], [ 0.555555555556, 0.111111111111, 0.10621977455 ], [ 0.722222222222, 0.111111111111, 0.10621977455 ], [ 0.888888888889, 0.111111111111, 0.10621977455 ], [ 0.055555555556, 0.277777777778, 0.10621977455 ], [ 0.222222222222, 0.277777777778, 0.10621977455 ], [ 0.388888888889, 0.277777777778, 0.10621977455 ], [ 0.555555555556, 0.277777777778, 0.10621977455 ], [ 0.722222222222, 0.277777777778, 0.10621977455 ], [ 0.888888888889, 0.277777777778, 0.10621977455 ], [ 0.055555555556, 0.444444444444, 0.10621977455 ], [ 0.222222222222, 0.444444444444, 0.10621977455 ], [ 0.388888888889, 0.444444444444, 0.10621977455 ], [ 0.555555555556, 0.444444444444, 0.10621977455 ], [ 0.722222222222, 0.444444444444, 0.10621977455 ], [ 0.888888888889, 0.444444444444, 0.10621977455 ], [ 0.055555555556, 0.611111111111, 0.10621977455 ], [ 0.222222222222, 0.611111111111, 0.10621977455 ], [ 0.388888888889, 0.611111111111, 0.10621977455 ], [ 0.555555555556, 0.611111111111, 0.10621977455 ], [ 0.722222222222, 0.611111111111, 0.10621977455 ], [ 0.888888888889, 0.611111111111, 0.10621977455 ], [ 0.055555555556, 0.777777777778, 0.10621977455 ], [ 0.222222222222, 0.777777777778, 0.10621977455 ], [ 0.388888888889, 0.777777777778, 0.10621977455 ], [ 0.555555555556, 0.777777777778, 0.10621977455 ], [ 0.722222222222, 0.777777777778, 0.10621977455 ], [ 0.888888888889, 0.777777777778, 0.10621977455 ], [ 0.055555555556, 0.944444444444, 0.10621977455 ], [ 0.222222222222, 0.944444444444, 0.10621977455 ], [ 0.388888888889, 0.944444444444, 0.10621977455 ], [ 0.555555555556, 0.944444444444, 0.10621977455 ], [ 0.722222222222, 0.944444444444, 0.10621977455 ], [ 0.888888888889, 0.944444444444, 0.10621977455 ], [ 0. , 0. , 0.212439549099], [ 0.166666666667, 0. , 0.212439549099], [ 0.333333333333, 0. , 0.212439549099], [ 0.5 , 0. , 0.212439549099], [ 0.666666666667, 0. , 0.212439549099], [ 0.833333333333, 0. , 0.212439549099], [-0. , 0.166666666667, 0.212439549099], [ 0.166666666667, 0.166666666667, 0.212439549099], [ 0.333333333333, 0.166666666667, 0.212439549099], [ 0.5 , 0.166666666667, 0.212439549099], [ 0.666666666667, 0.166666666667, 0.212439549099], [ 0.833333333333, 0.166666666667, 0.212439549099], [-0. , 0.333333333333, 0.212439549099], [ 0.166666666667, 0.333333333333, 0.212439549099], [ 0.333333333333, 0.333333333333, 0.212439549099], [ 0.5 , 0.333333333333, 0.212439549099], [ 0.666666666667, 0.333333333333, 0.212439549099], [ 0.833333333333, 0.333333333333, 0.212439549099], [-0. , 0.5 , 0.212439549099], [ 0.166666666667, 0.5 , 0.212439549099], [ 0.333333333333, 0.5 , 0.212439549099], [ 0.5 , 0.5 , 0.212439549099], [ 0.666666666667, 0.5 , 0.212439549099], [ 0.833333333333, 0.5 , 0.212439549099], [ 0. , 0.666666666667, 0.212439549099], [ 0.166666666667, 0.666666666667, 0.212439549099], [ 0.333333333333, 0.666666666667, 0.212439549099], [ 0.5 , 0.666666666667, 0.212439549099], [ 0.666666666667, 0.666666666667, 0.212439549099], [ 0.833333333333, 0.666666666667, 0.212439549099], [-0. , 0.833333333333, 0.212439549099], [ 0.166666666667, 0.833333333333, 0.212439549099], [ 0.333333333333, 0.833333333333, 0.212439549099], [ 0.5 , 0.833333333333, 0.212439549099], [ 0.666666666667, 0.833333333333, 0.212439549099], [ 0.833333333333, 0.833333333333, 0.212439549099], [ 0.111111111111, 0.055555555556, 0.318659323649], [ 0.277777777778, 0.055555555556, 0.318659323649], [ 0.444444444444, 0.055555555556, 0.318659323649], [ 0.611111111111, 0.055555555556, 0.318659323649], [ 0.777777777778, 0.055555555556, 0.318659323649], [ 0.944444444444, 0.055555555556, 0.318659323649], [ 0.111111111111, 0.222222222222, 0.318659323649], [ 0.277777777778, 0.222222222222, 0.318659323649], [ 0.444444444444, 0.222222222222, 0.318659323649], [ 0.611111111111, 0.222222222222, 0.318659323649], [ 0.777777777778, 0.222222222222, 0.318659323649], [ 0.944444444444, 0.222222222222, 0.318659323649], [ 0.111111111111, 0.388888888889, 0.318659323649], [ 0.277777777778, 0.388888888889, 0.318659323649], [ 0.444444444444, 0.388888888889, 0.318659323649], [ 0.611111111111, 0.388888888889, 0.318659323649], [ 0.777777777778, 0.388888888889, 0.318659323649], [ 0.944444444444, 0.388888888889, 0.318659323649], [ 0.111111111111, 0.555555555556, 0.318659323649], [ 0.277777777778, 0.555555555556, 0.318659323649], [ 0.444444444444, 0.555555555556, 0.318659323649], [ 0.611111111111, 0.555555555556, 0.318659323649], [ 0.777777777778, 0.555555555556, 0.318659323649], [ 0.944444444444, 0.555555555556, 0.318659323649], [ 0.111111111111, 0.722222222222, 0.318659323649], [ 0.277777777778, 0.722222222222, 0.318659323649], [ 0.444444444444, 0.722222222222, 0.318659323649], [ 0.611111111111, 0.722222222222, 0.318659323649], [ 0.777777777778, 0.722222222222, 0.318659323649], [ 0.944444444444, 0.722222222222, 0.318659323649], [ 0.111111111111, 0.888888888889, 0.318659323649], [ 0.277777777778, 0.888888888889, 0.318659323649], [ 0.444444444444, 0.888888888889, 0.318659323649], [ 0.611111111111, 0.888888888889, 0.318659323649], [ 0.777777777778, 0.888888888889, 0.318659323649], [ 0.944444444444, 0.888888888889, 0.318659323649], [ 0.055555555556, 0.111111111111, 0.424879098199], [ 0.222222222222, 0.111111111111, 0.424879098199], [ 0.388888888889, 0.111111111111, 0.424879098199], [ 0.555555555556, 0.111111111111, 0.424879098199], [ 0.722222222222, 0.111111111111, 0.424879098199], [ 0.888888888889, 0.111111111111, 0.424879098199], [ 0.055555555556, 0.277777777778, 0.424879098199], [ 0.222222222222, 0.277777777778, 0.424879098199], [ 0.388888888889, 0.277777777778, 0.424879098199], [ 0.555555555556, 0.277777777778, 0.424879098199], [ 0.722222222222, 0.277777777778, 0.424879098199], [ 0.888888888889, 0.277777777778, 0.424879098199], [ 0.055555555556, 0.444444444444, 0.424879098199], [ 0.222222222222, 0.444444444444, 0.424879098199], [ 0.388888888889, 0.444444444444, 0.424879098199], [ 0.555555555556, 0.444444444444, 0.424879098199], [ 0.722222222222, 0.444444444444, 0.424879098199], [ 0.888888888889, 0.444444444444, 0.424879098199], [ 0.055555555556, 0.611111111111, 0.424879098199], [ 0.222222222222, 0.611111111111, 0.424879098199], [ 0.388888888889, 0.611111111111, 0.424879098199], [ 0.555555555556, 0.611111111111, 0.424879098199], [ 0.722222222222, 0.611111111111, 0.424879098199], [ 0.888888888889, 0.611111111111, 0.424879098199], [ 0.055555555556, 0.777777777778, 0.424879098199], [ 0.222222222222, 0.777777777778, 0.424879098199], [ 0.388888888889, 0.777777777778, 0.424879098199], [ 0.555555555556, 0.777777777778, 0.424879098199], [ 0.722222222222, 0.777777777778, 0.424879098199], [ 0.888888888889, 0.777777777778, 0.424879098199], [ 0.055555555556, 0.944444444444, 0.424879098199], [ 0.222222222222, 0.944444444444, 0.424879098199], [ 0.388888888889, 0.944444444444, 0.424879098199], [ 0.555555555556, 0.944444444444, 0.424879098199], [ 0.722222222222, 0.944444444444, 0.424879098199], [ 0.888888888889, 0.944444444444, 0.424879098199], [ 0.833333333333, 0. , 0.531098872748], [ 0.666666666667, 0.166666666667, 0.531098872748], [ 0.5 , 0.333333333333, 0.531098872748], [ 0.333333333333, 0.5 , 0.531098872748], [ 0.166666666667, 0.666666666667, 0.531098872748], [ 0.666666666667, 0.666666666667, 0.531098872748], [-0. , 0.833333333333, 0.531098872748]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags bulk_configuration.addTags('Selection 0', [ 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]) # Morse Potential potentialSet = TremoloXPotentialSet(name='Pt-Morse') potentialSet.addParticleType(ParticleType.fromElement(Platinum)) potentialSet.addPotential(MorsePotential( 'Pt', 'Pt', r_0=2.897*Angstrom, k=1.6047*Angstrom**-1, E_0=0.7102*eV, r_i=6.5*Angstrom, r_cut=9.5*Angstrom) ) calculator = TremoloXCalculator(parameters=potentialSet) bulk_configuration.setCalculator(calculator) # ------------------------------------------------------------- # Optimize Geometry # ------------------------------------------------------------- fix_atom_indices_0 = [ 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] constraints = [FixAtomConstraints(fix_atom_indices_0)] bulk_configuration = OptimizeGeometry( bulk_configuration, max_forces=0.01*eV/Ang, max_steps=200, max_step_length=0.2*Ang, constraints=constraints, trajectory_filename=None, disable_stress=True, optimizer_method=LBFGS(), ) nlsave('initial.hdf5', bulk_configuration) nlprint(bulk_configuration)