# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Molecule Configuration # ------------------------------------------------------------- # Define elements elements = [Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen] # Define coordinates cartesian_coordinates = [[0.987524, -0.003838, -1.18508 ], [-0.020839, -0.022441, -0.751621], [-0.569312, 0.833015, -1.166929], [-0.514525, -0.932892, -1.115519], [0.020891, 0.022496, 0.751587], [0.568699, -0.833372, 1.166882], [0.515082, 0.932608, 1.115691], [-0.987522, 0.004424, 1.184988]]*Angstrom # Set up configuration molecule_configuration = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = TremoloXPotentialSet(name = 'Brenner_CH_2002') 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 = [], )) _potential = TersoffBrennerPairPotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), A = 10953.5441622*eV, Q = 0.313460296083*Angstrom, l = 4.74653906066*1/Angstrom, B1 = 12388.791978*eV, B2 = 17.567406465*eV, B3 = 30.7149320807*eV, mu1 = 4.7204523127*1/Angstrom, mu2 = 1.4332132499*1/Angstrom, mu3 = 1.3826912506*1/Angstrom, Re = 0.0*Angstrom, R1 = 1.7*Angstrom, R2 = 2.0*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), A = 32.817356*eV, Q = 0.3704716*Angstrom, l = 3.5362986*1/Angstrom, B1 = 29.632593*eV, B2 = 0.0*eV, B3 = 0.0*eV, mu1 = 1.7158922*1/Angstrom, mu2 = 0.0*1/Angstrom, mu3 = 0.0*1/Angstrom, Re = 0.0*Angstrom, R1 = 1.1*Angstrom, R2 = 1.7*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), A = 149.94099*eV, Q = 0.340776*Angstrom, l = 4.1025498*1/Angstrom, B1 = 32.355187*eV, B2 = 0.0*eV, B3 = 0.0*eV, mu1 = 1.4344581*1/Angstrom, mu2 = 0.0*1/Angstrom, mu3 = 0.0*1/Angstrom, Re = 0.0*Angstrom, R1 = 1.3*Angstrom, R2 = 1.8*Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), delta = 0.5, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), delta = 0.5, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), delta = 0.5, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), delta = 0.5, eta = 1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 0.0*1/Angstrom, L = 3.2, U = 3.7, rho1 = 0.0*Angstrom, rho2 = 0.0*Angstrom, x1 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f1 = numpy.array([-0.01, 0.0528, 0.09733, 0.37545, 2.0014, 8.0]), dfx1 = numpy.array([0.104, 0.17, 0.4, 1.406776, 6.056472, 20.240234]), dfxx1 = numpy.array([0.0, 0.37, 1.98, 4.508755, 16.147742, 43.901021]), x2 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f2 = numpy.array([-0.01, 0.0528, 0.09733, 0.271856, 0.416335, 1.0]), dfx2 = numpy.array([0.104, 0.17, 0.4, 0.488916, 0.25958, 2.831613]), dfxx2 = numpy.array([0.0, 0.37, 1.98, -0.866163, 1.170791, 10.239179]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, L = 3.2, U = 3.7, rho1 = 0.0*Angstrom, rho2 = 0.0*Angstrom, x1 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f1 = numpy.array([-0.01, 0.0528, 0.09733, 0.37545, 2.0014, 8.0]), dfx1 = numpy.array([0.104, 0.17, 0.4, 1.406776, 6.056472, 20.240234]), dfxx1 = numpy.array([0.0, 0.37, 1.98, 4.508755, 16.147742, 43.901021]), x2 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f2 = numpy.array([-0.01, 0.0528, 0.09733, 0.271856, 0.416335, 1.0]), dfx2 = numpy.array([0.104, 0.17, 0.4, 0.488916, 0.25958, 2.831613]), dfxx2 = numpy.array([0.0, 0.37, 1.98, -0.866163, 1.170791, 10.239179]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('C', []), beta = 1, alpha = 0.0*1/Angstrom, L = 3.2, U = 3.7, rho1 = 0.0*Angstrom, rho2 = 0.0*Angstrom, x1 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f1 = numpy.array([-0.01, 0.0528, 0.09733, 0.37545, 2.0014, 8.0]), dfx1 = numpy.array([0.104, 0.17, 0.4, 1.406776, 6.056472, 20.240234]), dfxx1 = numpy.array([0.0, 0.37, 1.98, 4.508755, 16.147742, 43.901021]), x2 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f2 = numpy.array([-0.01, 0.0528, 0.09733, 0.271856, 0.416335, 1.0]), dfx2 = numpy.array([0.104, 0.17, 0.4, 0.488916, 0.25958, 2.831613]), dfxx2 = numpy.array([0.0, 0.37, 1.98, -0.866163, 1.170791, 10.239179]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('H', []), beta = 1, alpha = 0.0*1/Angstrom, L = 3.2, U = 3.7, rho1 = 0.0*Angstrom, rho2 = 0.0*Angstrom, x1 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f1 = numpy.array([-0.01, 0.0528, 0.09733, 0.37545, 2.0014, 8.0]), dfx1 = numpy.array([0.104, 0.17, 0.4, 1.406776, 6.056472, 20.240234]), dfxx1 = numpy.array([0.0, 0.37, 1.98, 4.508755, 16.147742, 43.901021]), x2 = numpy.array([-1.0, -0.5, -0.333412, 0.0, 0.5, 1.0]), f2 = numpy.array([-0.01, 0.0528, 0.09733, 0.271856, 0.416335, 1.0]), dfx2 = numpy.array([0.104, 0.17, 0.4, 0.488916, 0.25958, 2.831613]), dfxx2 = numpy.array([0.0, 0.37, 1.98, -0.866163, 1.170791, 10.239179]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('H', []), beta = 0, alpha = 4, L = -1.0, U = -1.0, rho1 = 0.7415887*Angstrom, rho2 = 0.7415887*Angstrom, x1 = numpy.array([-1.0, -0.866025, -0.5, 0.0, 0.5, 1.0]), f1 = numpy.array([11.23587, 12.164186, 16.811574, 19.065124, 19.704059, 19.991787]), dfx1 = numpy.array([0.963483, 11.272285, 10.02705, 1.087747, 1.667291, 0.0]), dfxx1 = numpy.array([116.199658, 43.393534, -26.117077, -3.972742, -1.13749, 9.009242]), x2 = numpy.array([0, 1]), f2 = numpy.array([0, 0]), dfx2 = numpy.array([0, 0]), dfxx2 = numpy.array([0, 0]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), particleType3 = ParticleIdentifier('C', []), beta = 0, alpha = 0, L = -1.0, U = -1.0, rho1 = 0.7415887*Angstrom, rho2 = 1.09*Angstrom, x1 = numpy.array([-1.0, -0.866025, -0.5, 0.0, 0.5, 1.0]), f1 = numpy.array([11.23587, 12.164186, 16.811574, 19.065124, 19.704059, 19.991787]), dfx1 = numpy.array([0.963483, 11.272285, 10.02705, 1.087747, 1.667291, 0.0]), dfxx1 = numpy.array([116.199658, 43.393534, -26.117077, -3.972742, -1.13749, 9.009242]), x2 = numpy.array([0, 1]), f2 = numpy.array([0, 0]), dfx2 = numpy.array([0, 0]), dfxx2 = numpy.array([0, 0]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('H', []), beta = 0, alpha = 0, L = -1.0, U = -1.0, rho1 = 1.09*Angstrom, rho2 = 0.7415887*Angstrom, x1 = numpy.array([-1.0, -0.866025, -0.5, 0.0, 0.5, 1.0]), f1 = numpy.array([11.23587, 12.164186, 16.811574, 19.065124, 19.704059, 19.991787]), dfx1 = numpy.array([0.963483, 11.272285, 10.02705, 1.087747, 1.667291, 0.0]), dfxx1 = numpy.array([116.199658, 43.393534, -26.117077, -3.972742, -1.13749, 9.009242]), x2 = numpy.array([0, 1]), f2 = numpy.array([0, 0]), dfx2 = numpy.array([0, 0]), dfxx2 = numpy.array([0, 0]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential3( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('C', []), particleType3 = ParticleIdentifier('C', []), beta = 0, alpha = 0, L = -1.0, U = -1.0, rho1 = 1.09*Angstrom, rho2 = 1.09*Angstrom, x1 = numpy.array([-1.0, -0.866025, -0.5, 0.0, 0.5, 1.0]), f1 = numpy.array([11.23587, 12.164186, 16.811574, 19.065124, 19.704059, 19.991787]), dfx1 = numpy.array([0.963483, 11.272285, 10.02705, 1.087747, 1.667291, 0.0]), dfxx1 = numpy.array([116.199658, 43.393534, -26.117077, -3.972742, -1.13749, 9.009242]), x2 = numpy.array([0, 1]), f2 = numpy.array([0, 0]), dfx2 = numpy.array([0, 0]), dfxx2 = numpy.array([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, 0.0], [0.0, 0.0030267, 0.00317953, 0.0], [0.0078607, 0.00632625, 0.0, 0.0], [0.01612536, 0.0, 0.0, 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, 0.01, -0.12204215, -0.30758471], [0.20933673, -0.1251234, -0.30052917, 0.0], [-0.06444962, -0.29890525, 0.0, 0.0], [-0.30392755, 0.0, 0.0, 0.0]]), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerCorrectionPotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), activeTypes = [ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3]), z = numpy.array( [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] ), 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, 0.0216935, 0.00495861, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.02469883, -0.00597133, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947]], [[0.0, 0.0216935, 0.00495861, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0525, -0.00208875, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428, -0.0080428 ], [0.0, 0.00482478, 0.015, -0.01, -0.01168894, -0.01337788, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682], [0.0, 0.0, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838]], [[0.0, 0.02469883, -0.00597133, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.00482478, 0.015, -0.01, -0.01168894, -0.01337788, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682, -0.01506682], [0.0, 0.04722478, 0.011, 0.01985293, 0.01654411, 0.01323529, 0.00992647, 0.00661765, 0.00330882, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469]], [[0.0, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947, -0.05989947], [0.0, 0.0, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838, -0.06241838], [0.0, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469, -0.02235469], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 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 = TersoffBrennerCorrectionPotential2( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('H', []), activeTypes = [ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3]), z = numpy.array( [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] ), 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, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25, -0.25 ], [0.0, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125 ], [0.0, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065 ]], [[0.0, 0.0, 0.0, 0.0, 0.0, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389, -0.00452389], [0.0, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125, -0.125 ], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065, -0.1065 ], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 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 = TersoffBrennerCorrectionPotential2( particleType1 = ParticleIdentifier('H', []), particleType2 = ParticleIdentifier('H', []), activeTypes = [ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3]), z = numpy.array( [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] ), 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, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.12491596, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 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 = TersoffBrennerTorsionCorrectionPotential( particleType1 = ParticleIdentifier('C', []), particleType2 = ParticleIdentifier('C', []), activeTypes = [ParticleIdentifier('C', []), ], L = 2.0, U = 3.0, x = numpy.array([0, 1, 2, 3]), z = numpy.array( [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] ), 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, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, -0.03514004, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837, -0.00404837], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]], [[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 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) calculator.setInternalOrdering("default") calculator.setVerletListsDelta(0.25*Angstrom) molecule_configuration.setCalculator(calculator) molecule_configuration.update()