pyiron\_atomistics.atomistics.structure.atoms.Atoms =================================================== .. currentmodule:: pyiron_atomistics.atomistics.structure.atoms .. autoclass:: Atoms :members: :show-inheritance: :inherited-members: .. automethod:: __init__ .. rubric:: Methods .. autosummary:: ~Atoms.__init__ ~Atoms.add_high_symmetry_path ~Atoms.add_high_symmetry_points ~Atoms.add_tag ~Atoms.analyse_ovito_centro_symmetry ~Atoms.analyse_ovito_cna_adaptive ~Atoms.analyse_ovito_voronoi_volume ~Atoms.analyse_phonopy_equivalent_atoms ~Atoms.analyse_pyscal_centro_symmetry ~Atoms.analyse_pyscal_cna_adaptive ~Atoms.analyse_pyscal_diamond_structure ~Atoms.analyse_pyscal_steinhardt_parameter ~Atoms.analyse_pyscal_voronoi_volume ~Atoms.append ~Atoms.apply_strain ~Atoms.center ~Atoms.center_coordinates_in_unit_cell ~Atoms.close ~Atoms.cluster_analysis ~Atoms.convert_element ~Atoms.convert_formula ~Atoms.copy ~Atoms.create_line_mode_structure ~Atoms.edit ~Atoms.euler_rotate ~Atoms.extend ~Atoms.find_mic ~Atoms.find_neighbors_by_vector ~Atoms.from_dict ~Atoms.from_hdf ~Atoms.fromdict ~Atoms.get_all_distances ~Atoms.get_angle ~Atoms.get_angles ~Atoms.get_angular_momentum ~Atoms.get_array ~Atoms.get_atomic_numbers ~Atoms.get_bonds ~Atoms.get_calculator ~Atoms.get_cell ~Atoms.get_cell_lengths_and_angles ~Atoms.get_celldisp ~Atoms.get_center_of_mass ~Atoms.get_charges ~Atoms.get_chemical_elements ~Atoms.get_chemical_formula ~Atoms.get_chemical_indices ~Atoms.get_chemical_symbols ~Atoms.get_constraint ~Atoms.get_density ~Atoms.get_dihedral ~Atoms.get_dihedrals ~Atoms.get_dipole_moment ~Atoms.get_distance ~Atoms.get_distances ~Atoms.get_distances_array ~Atoms.get_equivalent_points ~Atoms.get_extended_positions ~Atoms.get_forces ~Atoms.get_global_number_of_atoms ~Atoms.get_high_symmetry_path ~Atoms.get_high_symmetry_points ~Atoms.get_initial_charges ~Atoms.get_initial_magnetic_moments ~Atoms.get_ir_reciprocal_mesh ~Atoms.get_kinetic_energy ~Atoms.get_kinetic_stress ~Atoms.get_kinetic_stresses ~Atoms.get_magnetic_moment ~Atoms.get_magnetic_moments ~Atoms.get_majority_species ~Atoms.get_masses ~Atoms.get_masses_dof ~Atoms.get_momenta ~Atoms.get_moments_of_inertia ~Atoms.get_neighborhood ~Atoms.get_neighbors ~Atoms.get_neighbors_by_distance ~Atoms.get_number_of_atoms ~Atoms.get_number_of_degrees_of_freedom ~Atoms.get_number_of_species ~Atoms.get_number_species_atoms ~Atoms.get_numbers_of_neighbors_in_sphere ~Atoms.get_parent_basis ~Atoms.get_parent_symbols ~Atoms.get_pbc ~Atoms.get_positions ~Atoms.get_potential_energies ~Atoms.get_potential_energy ~Atoms.get_primitive_cell ~Atoms.get_properties ~Atoms.get_reciprocal_cell ~Atoms.get_scaled_positions ~Atoms.get_shell_matrix ~Atoms.get_spacegroup ~Atoms.get_species_objects ~Atoms.get_species_symbols ~Atoms.get_spherical_coordinates ~Atoms.get_stress ~Atoms.get_stresses ~Atoms.get_symmetry ~Atoms.get_symmetry_dataset ~Atoms.get_tags ~Atoms.get_temperature ~Atoms.get_total_energy ~Atoms.get_velocities ~Atoms.get_vertical_length ~Atoms.get_volume ~Atoms.get_voronoi_volume ~Atoms.get_wrapped_coordinates ~Atoms.group_points_by_symmetry ~Atoms.has ~Atoms.is_skewed ~Atoms.iterimages ~Atoms.new_array ~Atoms.numbers_to_elements ~Atoms.occupy_lattice ~Atoms.plot3d ~Atoms.pop ~Atoms.pos_xyz ~Atoms.rattle ~Atoms.refine_cell ~Atoms.repeat ~Atoms.repeat_points ~Atoms.reset_absolute ~Atoms.rotate ~Atoms.rotate_dihedral ~Atoms.scaled_pos_xyz ~Atoms.select_index ~Atoms.select_parent_index ~Atoms.set_absolute ~Atoms.set_angle ~Atoms.set_array ~Atoms.set_atomic_numbers ~Atoms.set_calculator ~Atoms.set_cell ~Atoms.set_celldisp ~Atoms.set_center_of_mass ~Atoms.set_chemical_symbols ~Atoms.set_constraint ~Atoms.set_dihedral ~Atoms.set_distance ~Atoms.set_initial_charges ~Atoms.set_initial_magnetic_moments ~Atoms.set_masses ~Atoms.set_momenta ~Atoms.set_pbc ~Atoms.set_positions ~Atoms.set_relative ~Atoms.set_repeat ~Atoms.set_scaled_positions ~Atoms.set_species ~Atoms.set_tags ~Atoms.set_velocities ~Atoms.symmetrize_vectors ~Atoms.to_ase ~Atoms.to_dict ~Atoms.to_hdf ~Atoms.to_ovito ~Atoms.to_pymatgen ~Atoms.to_pyscal_system ~Atoms.todict ~Atoms.translate ~Atoms.wrap ~Atoms.write .. rubric:: Attributes .. autosummary:: ~Atoms.analyse ~Atoms.ase_objtype ~Atoms.calc ~Atoms.cell ~Atoms.constraints ~Atoms.elements ~Atoms.number_of_lattice_vectors ~Atoms.numbers ~Atoms.pbc ~Atoms.positions ~Atoms.species ~Atoms.spins ~Atoms.symbols ~Atoms.velocities