def test4(): atoms = SWNTGenerator(10, 5, nz=2).atoms atoms.assign_unique_ids() atoms.update_attrs() atoms.center_centroid() print(atoms.centroid) bond = atoms.get_atom(atoms.Natoms // 2).bonds[0] print(bond) print('bond.atoms.coords:\n{}'.format(bond.atoms.coords)) bond_centroid = bond.centroid print('bond.centroid: {}'.format(bond.centroid)) rot_axis = Vector(p0=[0, 0, bond_centroid.z], p=bond_centroid.p) bond.rotate(angle=np.pi/2, axis=rot_axis) print(bond) print('bond.atoms.coords:\n{}'.format(bond.atoms.coords)) assert_true(np.allclose(bond_centroid, bond.centroid))
def test4(): atoms = SWNTGenerator(10, 5, nz=2).atoms atoms.assign_unique_ids() atoms.update_attrs() atoms.center_centroid() print(atoms.centroid) bond = atoms.get_atom(atoms.Natoms // 2).bonds[0] print(bond) print("bond.atoms.coords:\n{}".format(bond.atoms.coords)) bond_centroid = bond.centroid print("bond.centroid: {}".format(bond.centroid)) rot_axis = Vector(p0=[0, 0, bond_centroid.z], p=bond_centroid.p) bond.rotate(angle=np.pi / 2, axis=rot_axis) print(bond) print("bond.atoms.coords:\n{}".format(bond.atoms.coords)) assert_true(np.allclose(bond_centroid, bond.centroid))
def test3(): atoms = SWNTGenerator(n=20, m=0, nz=2).atoms assert_equal(atoms.Natoms, 160) atoms.assign_unique_ids() atoms.update_attrs() print(np.degrees(atoms.bonds.mean_length)) print(np.degrees(atoms.bonds.mean_angle)) atom0 = atoms[0] atom0bonds = atom0.bonds print('atom0: {}'.format(atom0)) print('atom0.r: {}'.format(atom0.r)) for NN in atom0.NN: print('NN.r: {}'.format(NN.r)) print(atom0bonds.atoms.Natoms) print(atom0bonds.atoms.CM) print('atoms.bonds.Nbonds: {}'.format(atoms.bonds.Nbonds)) print('atoms.bonds.atoms.Natoms: {}'.format(atoms.bonds.atoms.Natoms))
def test3(): atoms = SWNTGenerator(n=20, m=0, nz=2).atoms assert_equal(atoms.Natoms, 160) atoms.assign_unique_ids() atoms.update_attrs() print(np.degrees(atoms.bonds.mean_length)) print(np.degrees(atoms.bonds.mean_angle)) atom0 = atoms[0] atom0bonds = atom0.bonds print("atom0: {}".format(atom0)) print("atom0.r: {}".format(atom0.r)) for NN in atom0.NN: print("NN.r: {}".format(NN.r)) print(atom0bonds.atoms.Natoms) print(atom0bonds.atoms.CM) print("atoms.bonds.Nbonds: {}".format(atoms.bonds.Nbonds)) print("atoms.bonds.atoms.Natoms: {}".format(atoms.bonds.atoms.Natoms))
def test2(): atoms = SWNTGenerator(n=10, m=10, nz=3).atoms atoms.assign_unique_ids() atoms.update_attrs()