# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Molecule Configuration # ------------------------------------------------------------- # Define elements elements = [Carbon, Silicon, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates cartesian_coordinates = [[ 0.309666700862, 0.758525407442, -0.437934848174], [-0.316999965805, -0.776488164702, 0.448305650913], [-1.74699986322 , -0.776488164702, 0.448305650913], [ 0.159666666667, -1.944078191668, -0.225802765459], [ 0.159666666667, -0.776488164702, 1.796522483657], [ 1.399666622667, 0.758525407442, -0.437934848174], [-0.053666606407, 0.758525407442, -1.465596629776], [-0.053666606407, 1.648506616808, 0.075896042627]]*Angstrom # Set up configuration molecule_configuration = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = TremoloXPotentialSet(name = 'Dyson_CHSi_1999') potentialSet.addParticleType(ParticleType( symbol = 'C', mass = 12.0107*atomic_mass_unit, charge = None, sigma = None, sigma14 = None, epsilon = None, epsilon14 = None, atomicNumber = 6, tags = [], )) potentialSet.addParticleType(ParticleType( symbol = 'H', mass = 1.00794*atomic_mass_unit, charge = None, sigma = None, sigma14 = None, epsilon = None, epsilon14 = None, atomicNumber = 1, tags = [], )) potentialSet.addParticleType(ParticleType( symbol = 'Si', mass = 28.0855*atomic_mass_unit, charge = None, sigma = None, sigma14 = None, epsilon = None, epsilon14 = None, atomicNumber = 14, tags = [], )) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), A = 1865.44920213*eV, B = 543.974039639*eV, l = 2.46687049113*1/Angstrom, mu = 1.74955353981*1/Angstrom, Re = 2.197*Angstrom, R1 = 2.65*Angstrom, R2 = 2.95*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), A = 1614.45185475*eV, B = 437.741074091*eV, l = 2.93316906025*1/Angstrom, mu = 1.96593100553*1/Angstrom, Re = 1.763*Angstrom, R1 = 2.2*Angstrom, R2 = 2.5*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), A = 323.519301143*eV, B = 80.0200987432*eV, l = 2.93627564101*1/Angstrom, mu = 1.61537967817*1/Angstrom, Re = 1.51*Angstrom, R1 = 1.65*Angstrom, R2 = 2.2*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), A = 518.369615293*eV, B = 328.020573367*eV, l = 2.40935676063*1/Angstrom, mu = 1.86771841909*1/Angstrom, Re = 1.315*Angstrom, R1 = 1.7*Angstrom, R2 = 2.0*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), A = 294.451935403*eV, B = 90.0948966226*eV, l = 3.65169132161*1/Angstrom, mu = 2.10036312068*1/Angstrom, Re = 1.1199*Angstrom, R1 = 1.3*Angstrom, R2 = 1.8*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), A = 80.0703477291*eV, B = 31.3793415132*eV, l = 4.20752366731*1/Angstrom, mu = 1.7956314729*1/Angstrom, Re = 0.74144*Angstrom, R1 = 1.1*Angstrom, R2 = 1.7*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), delta = 0.78, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), delta = 0.78, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), delta = 0.78, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('Si', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('Si', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), delta = 0.80469, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('Si', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 4.0, g_c = 0.0, g_d = 1.0, g_h = 0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('Si', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.011304, g_c = 19.0, g_d = 2.5, g_h = -1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 0.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential5( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 3.0*1/Angstrom, g_a = 0.01, g_c = 14.0, g_d = 2.1, activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), h = numpy.array([[-0. , -0.5 , -1. , -1. , -0. , -0. ], [-0. , -0.049, -0.45 , -0.68 , -0. , -0. ], [-0.04 , -0.436, -0.75 , -0. , -0. , -0. ], [-0.35 , -0.65 , -0.85 , -0. , -0. , -0. ], [-0.6 , -0.8 , -0. , -0. , -0. , -0. ], [-0. , -0. , -0. , -0. , -0. , -0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ], x = numpy.array([0, 1, 2, 3]), y = numpy.array([0, 1, 2, 3]), f = numpy.array([[ 0. , 0. , 0. , 0. ], [ 0. , -0.0175, 0.0115, 0. ], [-0.007 , 0.0118, 0. , 0. ], [ 0.0119, 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ], x = numpy.array([ 0., 1., 2., 3.]), y = numpy.array([ 0., 1., 2., 3.]), f = numpy.array([[ 0. , -0.1792, -0.2407, -0.3323], [-0.076 , -0.2477, -0.3321, 0. ], [-0.2163, -0.332 , 0. , 0. ], [-0.3375, 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ParticleIdentifier('Si', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[ 0. , 0.07 , 0.05 , 0. , 0. , 0. ], [ 0.095, 0.17 , 0.05 , 0. , 0. , 0. ], [ 0.025, 0.07 , 0. , 0. , 0. , 0. ], [ 0.05 , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('H', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ParticleIdentifier('Si', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[ 0. , 0. , -0.115, -0.08 , 0. , 0. ], [-0.125, -0.03 , -0.15 , 0. , 0. , 0. ], [-0.058, -0.138, 0. , 0. , 0. , 0. ], [-0.142, 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ParticleIdentifier('Si', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[ 0. , 0.039, 0.005, 0. , 0. , 0. ], [ 0.02 , 0.2 , 0.11 , 0. , 0. , 0. ], [ 0.01 , 0.012, 0. , 0. , 0. , 0. ], [ 0.09 , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('Si', []), activeTypes1 = [ParticleIdentifier('H', []), ], activeTypes2 = [ParticleIdentifier('C', []), ParticleIdentifier('Si', []), ], x = numpy.array([0, 1, 2, 3, 4, 5]), y = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[ 0. , 0.042, 0.09 , 0. , 0. , 0. ], [ 0.15 , 0.005, 0.045, 0. , 0. , 0. ], [-0.007, -0.04 , 0. , 0. , 0. , 0. ], [ 0.09 , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerCorrectionPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), activeTypes = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3, 4, 5]), z = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0.055 , 0. , 0. , 0. , 0. ], [ 0. , 0.016 , -0.02225, -0.02225, -0.02225, -0.02225], [ 0. , -0.061 , -0.061 , -0.061 , -0.061 , -0.061 ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0.055 , 0. , 0. , 0. , 0. ], [ 0. , 0.07555, 0.0037 , 0.0037 , 0.0037 , 0.0037 ], [ 0. , 0.0063 , -0.01775, -0.01775, -0.01775, -0.01775], [ 0. , -0.0565 , -0.0565 , -0.0565 , -0.0565 , -0.0565 ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0.016 , -0.02225, -0.02225, -0.02225, -0.02225], [ 0. , 0.0063 , -0.01775, -0.01775, -0.01775, -0.01775], [ 0. , 0.0375 , 0. , 0. , 0. , 0. ], [ 0. , -0.02325, -0.02325, -0.02325, -0.02325, -0.02325], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , -0.061 , -0.061 , -0.061 , -0.061 , -0.061 ], [ 0. , -0.0565 , -0.0565 , -0.0565 , -0.0565 , -0.0565 ], [ 0. , -0.02325, -0.02325, -0.02325, -0.02325, -0.02325], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerCorrectionPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('Si', []), activeTypes = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3, 4, 5]), z = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , -0.0075, -0.0075, 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0.03 , 0.0075, 0. , 0. , 0. ], [ 0. , 0. , -0.0125, 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , -0.0075, -0.0075, 0. , 0. , 0. ], [ 0. , 0. , -0.0125, 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerCorrectionPotential( particleType1 = ParticleIdentifier('Si', []), particleType2 = ParticleIdentifier('C', []), activeTypes = [ParticleIdentifier('Si', []), ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3, 4, 5]), z = numpy.array([0, 1, 2, 3, 4, 5]), f = numpy.array([[[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0.0625, 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , -0.075 , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0.0725, 0. , 0. , 0. , 0. ], [ 0. , -0.0175, -0.02 , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , -0.075 , 0. , 0. , 0. , 0. ], [ 0. , -0.0175, -0.02 , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]], [[ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. ]]]), ) potentialSet.addPotential(_potential) calculator = TremoloXCalculator(parameters=potentialSet) molecule_configuration.setCalculator(calculator) molecule_configuration.update()