pyiron\_atomistics.sphinx.base.SphinxBase
=========================================

.. currentmodule:: pyiron_atomistics.sphinx.base

.. autoclass:: SphinxBase
   :members:
   :show-inheritance:
   :inherited-members:

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~SphinxBase.__init__
      ~SphinxBase.animate_structure
      ~SphinxBase.animate_structures
      ~SphinxBase.calc_md
      ~SphinxBase.calc_minimize
      ~SphinxBase.calc_static
      ~SphinxBase.check_if_job_exists
      ~SphinxBase.check_setup
      ~SphinxBase.check_vasp_potentials
      ~SphinxBase.clear_job
      ~SphinxBase.collect_errors
      ~SphinxBase.collect_logfiles
      ~SphinxBase.collect_output
      ~SphinxBase.collect_structures
      ~SphinxBase.collect_warnings
      ~SphinxBase.compress
      ~SphinxBase.continue_with_final_structure
      ~SphinxBase.continue_with_restart_files
      ~SphinxBase.convergence_check
      ~SphinxBase.copy
      ~SphinxBase.copy_file_to_working_directory
      ~SphinxBase.copy_template
      ~SphinxBase.copy_to
      ~SphinxBase.create_job
      ~SphinxBase.create_pipeline
      ~SphinxBase.db_entry
      ~SphinxBase.decompress
      ~SphinxBase.drop_status_to_aborted
      ~SphinxBase.from_dict
      ~SphinxBase.from_directory
      ~SphinxBase.from_hdf
      ~SphinxBase.from_hdf_args
      ~SphinxBase.get
      ~SphinxBase.get_bader_charges
      ~SphinxBase.get_bader_volumes
      ~SphinxBase.get_calculate_function
      ~SphinxBase.get_charge_density
      ~SphinxBase.get_density_of_states
      ~SphinxBase.get_electronic_structure
      ~SphinxBase.get_electrostatic_potential
      ~SphinxBase.get_encut
      ~SphinxBase.get_final_structure
      ~SphinxBase.get_from_table
      ~SphinxBase.get_input_parameter_dict
      ~SphinxBase.get_job_id
      ~SphinxBase.get_k_mesh_by_cell
      ~SphinxBase.get_kpoints
      ~SphinxBase.get_magnetic_moments
      ~SphinxBase.get_n_ir_reciprocal_points
      ~SphinxBase.get_neighbors
      ~SphinxBase.get_neighbors_snapshots
      ~SphinxBase.get_output_parameter_dict
      ~SphinxBase.get_scf_group
      ~SphinxBase.get_structure
      ~SphinxBase.get_structure_group
      ~SphinxBase.get_valence_and_total_charge_density
      ~SphinxBase.get_version_float
      ~SphinxBase.get_workdir_file
      ~SphinxBase.gui
      ~SphinxBase.inspect
      ~SphinxBase.instantiate
      ~SphinxBase.interactive_close
      ~SphinxBase.interactive_fetch
      ~SphinxBase.interactive_flush
      ~SphinxBase.is_compressed
      ~SphinxBase.is_master_id
      ~SphinxBase.is_self_archived
      ~SphinxBase.iter_structures
      ~SphinxBase.job_file_name
      ~SphinxBase.kill
      ~SphinxBase.list_all
      ~SphinxBase.list_childs
      ~SphinxBase.list_files
      ~SphinxBase.list_groups
      ~SphinxBase.list_nodes
      ~SphinxBase.list_potentials
      ~SphinxBase.load
      ~SphinxBase.load_basis_group
      ~SphinxBase.load_default_groups
      ~SphinxBase.load_default_input
      ~SphinxBase.load_guess_group
      ~SphinxBase.load_hamilton_group
      ~SphinxBase.load_main_group
      ~SphinxBase.load_species_group
      ~SphinxBase.load_structure_group
      ~SphinxBase.map
      ~SphinxBase.modify_kpoints
      ~SphinxBase.move_to
      ~SphinxBase.nbands_convergence_check
      ~SphinxBase.refresh_job_status
      ~SphinxBase.relocate_hdf5
      ~SphinxBase.remove
      ~SphinxBase.remove_and_reset_id
      ~SphinxBase.remove_child
      ~SphinxBase.rename
      ~SphinxBase.reset_job_id
      ~SphinxBase.restart
      ~SphinxBase.restart_for_band_structure_calculations
      ~SphinxBase.restart_from_charge_density
      ~SphinxBase.restart_from_wave_functions
      ~SphinxBase.run
      ~SphinxBase.run_addon
      ~SphinxBase.run_if_interactive
      ~SphinxBase.run_if_interactive_non_modal
      ~SphinxBase.run_if_modal
      ~SphinxBase.run_if_refresh
      ~SphinxBase.run_if_scheduler
      ~SphinxBase.run_static
      ~SphinxBase.run_time_to_db
      ~SphinxBase.save
      ~SphinxBase.save_output
      ~SphinxBase.self_archive
      ~SphinxBase.self_unarchive
      ~SphinxBase.set_check_overlap
      ~SphinxBase.set_convergence_precision
      ~SphinxBase.set_empty_states
      ~SphinxBase.set_encut
      ~SphinxBase.set_exchange_correlation_functional
      ~SphinxBase.set_input_to_read_only
      ~SphinxBase.set_kpoints
      ~SphinxBase.set_mixing_parameters
      ~SphinxBase.set_occupancy_smearing
      ~SphinxBase.show_hdf
      ~SphinxBase.signal_intercept
      ~SphinxBase.store_structure
      ~SphinxBase.suspend
      ~SphinxBase.to_dict
      ~SphinxBase.to_hdf
      ~SphinxBase.to_object
      ~SphinxBase.trajectory
      ~SphinxBase.transfer_from_remote
      ~SphinxBase.transform_structures
      ~SphinxBase.update_master
      ~SphinxBase.update_sphinx
      ~SphinxBase.validate_ready_to_run
      ~SphinxBase.view_structure
      ~SphinxBase.write_input
      ~SphinxBase.write_traj
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~SphinxBase.calculate_kwargs
      ~SphinxBase.child_ids
      ~SphinxBase.content
      ~SphinxBase.database_entry
      ~SphinxBase.encut
      ~SphinxBase.exchange_correlation_functional
      ~SphinxBase.exclude_groups_hdf
      ~SphinxBase.exclude_nodes_hdf
      ~SphinxBase.executable
      ~SphinxBase.executor_type
      ~SphinxBase.files
      ~SphinxBase.files_to_compress
      ~SphinxBase.files_to_remove
      ~SphinxBase.fix_spin_constraint
      ~SphinxBase.fix_symmetry
      ~SphinxBase.id
      ~SphinxBase.id_pyi_to_spx
      ~SphinxBase.id_spx_to_pyi
      ~SphinxBase.job_id
      ~SphinxBase.job_info_str
      ~SphinxBase.job_name
      ~SphinxBase.job_type
      ~SphinxBase.k_mesh_center_shift
      ~SphinxBase.k_mesh_spacing
      ~SphinxBase.kpoint_mesh
      ~SphinxBase.logger
      ~SphinxBase.master_id
      ~SphinxBase.name
      ~SphinxBase.number_of_structures
      ~SphinxBase.parent_id
      ~SphinxBase.path
      ~SphinxBase.plane_wave_cutoff
      ~SphinxBase.potential
      ~SphinxBase.potential_list
      ~SphinxBase.potential_view
      ~SphinxBase.project
      ~SphinxBase.project_hdf5
      ~SphinxBase.queue_id
      ~SphinxBase.reduce_kpoint_symmetry
      ~SphinxBase.restart_file_dict
      ~SphinxBase.restart_file_list
      ~SphinxBase.server
      ~SphinxBase.spin_constraints
      ~SphinxBase.status
      ~SphinxBase.structure
      ~SphinxBase.version
      ~SphinxBase.working_directory
      ~SphinxBase.xc