pyiron\_atomistics.sphinx.sphinx.Sphinx ======================================= .. currentmodule:: pyiron_atomistics.sphinx.sphinx .. autoclass:: Sphinx :members: :show-inheritance: :inherited-members: .. automethod:: __init__ .. rubric:: Methods .. autosummary:: ~Sphinx.__init__ ~Sphinx.animate_structure ~Sphinx.animate_structures ~Sphinx.calc_md ~Sphinx.calc_minimize ~Sphinx.calc_static ~Sphinx.check_if_job_exists ~Sphinx.check_setup ~Sphinx.check_vasp_potentials ~Sphinx.clear_job ~Sphinx.collect_errors ~Sphinx.collect_logfiles ~Sphinx.collect_output ~Sphinx.collect_structures ~Sphinx.collect_warnings ~Sphinx.compress ~Sphinx.continue_with_final_structure ~Sphinx.continue_with_restart_files ~Sphinx.convergence_check ~Sphinx.copy ~Sphinx.copy_file_to_working_directory ~Sphinx.copy_template ~Sphinx.copy_to ~Sphinx.create_job ~Sphinx.create_pipeline ~Sphinx.db_entry ~Sphinx.decompress ~Sphinx.drop_status_to_aborted ~Sphinx.from_dict ~Sphinx.from_directory ~Sphinx.from_hdf ~Sphinx.from_hdf_args ~Sphinx.get ~Sphinx.get_bader_charges ~Sphinx.get_bader_volumes ~Sphinx.get_calculate_function ~Sphinx.get_charge_density ~Sphinx.get_density_of_states ~Sphinx.get_electronic_structure ~Sphinx.get_electrostatic_potential ~Sphinx.get_encut ~Sphinx.get_final_structure ~Sphinx.get_from_table ~Sphinx.get_input_parameter_dict ~Sphinx.get_job_id ~Sphinx.get_k_mesh_by_cell ~Sphinx.get_kpoints ~Sphinx.get_magnetic_moments ~Sphinx.get_n_ir_reciprocal_points ~Sphinx.get_neighbors ~Sphinx.get_neighbors_snapshots ~Sphinx.get_output_parameter_dict ~Sphinx.get_scf_group ~Sphinx.get_structure ~Sphinx.get_structure_group ~Sphinx.get_valence_and_total_charge_density ~Sphinx.get_version_float ~Sphinx.get_workdir_file ~Sphinx.gui ~Sphinx.inspect ~Sphinx.instantiate ~Sphinx.interactive_atom_spin_constraints_getter ~Sphinx.interactive_atom_spins_getter ~Sphinx.interactive_cell_organizer ~Sphinx.interactive_cells_getter ~Sphinx.interactive_cells_setter ~Sphinx.interactive_close ~Sphinx.interactive_collect ~Sphinx.interactive_computation_time_getter ~Sphinx.interactive_energy_pot_getter ~Sphinx.interactive_energy_tot_getter ~Sphinx.interactive_fetch ~Sphinx.interactive_flush ~Sphinx.interactive_forces_getter ~Sphinx.interactive_index_organizer ~Sphinx.interactive_indices_getter ~Sphinx.interactive_indices_setter ~Sphinx.interactive_initialize_interface ~Sphinx.interactive_is_activated ~Sphinx.interactive_magmom_organizer ~Sphinx.interactive_magnetic_forces_getter ~Sphinx.interactive_open ~Sphinx.interactive_positions_getter ~Sphinx.interactive_positions_organizer ~Sphinx.interactive_positions_setter ~Sphinx.interactive_pressures_getter ~Sphinx.interactive_spin_constraints_getter ~Sphinx.interactive_spin_constraints_setter ~Sphinx.interactive_spins_getter ~Sphinx.interactive_steps_getter ~Sphinx.interactive_store_in_cache ~Sphinx.interactive_stress_getter ~Sphinx.interactive_structure_setter ~Sphinx.interactive_temperatures_getter ~Sphinx.interactive_time_getter ~Sphinx.interactive_unwrapped_positions_getter ~Sphinx.interactive_volume_getter ~Sphinx.is_compressed ~Sphinx.is_master_id ~Sphinx.is_self_archived ~Sphinx.iter_structures ~Sphinx.job_file_name ~Sphinx.kill ~Sphinx.list_all ~Sphinx.list_childs ~Sphinx.list_files ~Sphinx.list_groups ~Sphinx.list_nodes ~Sphinx.list_potentials ~Sphinx.load ~Sphinx.load_basis_group ~Sphinx.load_default_groups ~Sphinx.load_default_input ~Sphinx.load_guess_group ~Sphinx.load_hamilton_group ~Sphinx.load_main_group ~Sphinx.load_species_group ~Sphinx.load_structure_group ~Sphinx.map ~Sphinx.modify_kpoints ~Sphinx.move_to ~Sphinx.nbands_convergence_check ~Sphinx.refresh_job_status ~Sphinx.relocate_hdf5 ~Sphinx.remove ~Sphinx.remove_and_reset_id ~Sphinx.remove_child ~Sphinx.rename ~Sphinx.reset_job_id ~Sphinx.restart ~Sphinx.restart_for_band_structure_calculations ~Sphinx.restart_from_charge_density ~Sphinx.restart_from_wave_functions ~Sphinx.run ~Sphinx.run_addon ~Sphinx.run_if_interactive ~Sphinx.run_if_interactive_non_modal ~Sphinx.run_if_modal ~Sphinx.run_if_refresh ~Sphinx.run_if_scheduler ~Sphinx.run_static ~Sphinx.run_time_to_db ~Sphinx.save ~Sphinx.save_output ~Sphinx.self_archive ~Sphinx.self_unarchive ~Sphinx.set_check_overlap ~Sphinx.set_convergence_precision ~Sphinx.set_empty_states ~Sphinx.set_encut ~Sphinx.set_exchange_correlation_functional ~Sphinx.set_input_to_read_only ~Sphinx.set_kpoints ~Sphinx.set_mixing_parameters ~Sphinx.set_occupancy_smearing ~Sphinx.show_hdf ~Sphinx.signal_intercept ~Sphinx.species_from_hdf ~Sphinx.store_structure ~Sphinx.suspend ~Sphinx.to_dict ~Sphinx.to_hdf ~Sphinx.to_object ~Sphinx.trajectory ~Sphinx.transfer_from_remote ~Sphinx.transform_structures ~Sphinx.update_master ~Sphinx.update_sphinx ~Sphinx.validate_ready_to_run ~Sphinx.view_structure ~Sphinx.write_input ~Sphinx.write_traj .. rubric:: Attributes .. autosummary:: ~Sphinx.calculate_kwargs ~Sphinx.child_ids ~Sphinx.content ~Sphinx.current_structure ~Sphinx.database_entry ~Sphinx.encut ~Sphinx.exchange_correlation_functional ~Sphinx.exclude_groups_hdf ~Sphinx.exclude_nodes_hdf ~Sphinx.executable ~Sphinx.executor_type ~Sphinx.files ~Sphinx.files_to_compress ~Sphinx.files_to_remove ~Sphinx.fix_spin_constraint ~Sphinx.fix_symmetry ~Sphinx.id ~Sphinx.id_pyi_to_spx ~Sphinx.id_spx_to_pyi ~Sphinx.initial_structure ~Sphinx.interactive_enforce_structure_reset ~Sphinx.interactive_flush_frequency ~Sphinx.interactive_write_frequency ~Sphinx.job_id ~Sphinx.job_info_str ~Sphinx.job_name ~Sphinx.job_type ~Sphinx.k_mesh_center_shift ~Sphinx.k_mesh_spacing ~Sphinx.kpoint_mesh ~Sphinx.logger ~Sphinx.master_id ~Sphinx.name ~Sphinx.number_of_structures ~Sphinx.parent_id ~Sphinx.path ~Sphinx.plane_wave_cutoff ~Sphinx.potential ~Sphinx.potential_list ~Sphinx.potential_view ~Sphinx.project ~Sphinx.project_hdf5 ~Sphinx.queue_id ~Sphinx.reduce_kpoint_symmetry ~Sphinx.restart_file_dict ~Sphinx.restart_file_list ~Sphinx.server ~Sphinx.spin_constraints ~Sphinx.status ~Sphinx.structure ~Sphinx.version ~Sphinx.working_directory ~Sphinx.xc