pyiron\_atomistics.lammps.lammps.Lammps
=======================================

.. currentmodule:: pyiron_atomistics.lammps.lammps

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

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~Lammps.__init__
      ~Lammps.animate_structure
      ~Lammps.animate_structures
      ~Lammps.calc_md
      ~Lammps.calc_minimize
      ~Lammps.calc_static
      ~Lammps.calc_vcsgc
      ~Lammps.check_if_job_exists
      ~Lammps.check_setup
      ~Lammps.clear_bonds
      ~Lammps.clear_job
      ~Lammps.collect_logfiles
      ~Lammps.collect_output
      ~Lammps.collect_structures
      ~Lammps.compress
      ~Lammps.continue_with_final_structure
      ~Lammps.continue_with_restart_files
      ~Lammps.convergence_check
      ~Lammps.copy
      ~Lammps.copy_file_to_working_directory
      ~Lammps.copy_template
      ~Lammps.copy_to
      ~Lammps.create_job
      ~Lammps.create_pipeline
      ~Lammps.db_entry
      ~Lammps.decompress
      ~Lammps.define_bonds
      ~Lammps.drop_status_to_aborted
      ~Lammps.enable_h5md
      ~Lammps.from_dict
      ~Lammps.from_hdf
      ~Lammps.from_hdf_args
      ~Lammps.get
      ~Lammps.get_calculate_function
      ~Lammps.get_final_structure
      ~Lammps.get_from_table
      ~Lammps.get_input_parameter_dict
      ~Lammps.get_job_id
      ~Lammps.get_neighbors
      ~Lammps.get_neighbors_snapshots
      ~Lammps.get_output_parameter_dict
      ~Lammps.get_potentials_for_structure
      ~Lammps.get_structure
      ~Lammps.get_workdir_file
      ~Lammps.gui
      ~Lammps.inspect
      ~Lammps.instantiate
      ~Lammps.interactive_atom_spin_constraints_getter
      ~Lammps.interactive_atom_spins_getter
      ~Lammps.interactive_cell_organizer
      ~Lammps.interactive_cells_getter
      ~Lammps.interactive_cells_setter
      ~Lammps.interactive_close
      ~Lammps.interactive_collect
      ~Lammps.interactive_computation_time_getter
      ~Lammps.interactive_energy_pot_getter
      ~Lammps.interactive_energy_tot_getter
      ~Lammps.interactive_execute
      ~Lammps.interactive_fetch
      ~Lammps.interactive_flush
      ~Lammps.interactive_forces_getter
      ~Lammps.interactive_index_organizer
      ~Lammps.interactive_indices_getter
      ~Lammps.interactive_indices_setter
      ~Lammps.interactive_initialize_interface
      ~Lammps.interactive_is_activated
      ~Lammps.interactive_magmom_organizer
      ~Lammps.interactive_magnetic_forces_getter
      ~Lammps.interactive_open
      ~Lammps.interactive_positions_getter
      ~Lammps.interactive_positions_organizer
      ~Lammps.interactive_positions_setter
      ~Lammps.interactive_pressures_getter
      ~Lammps.interactive_spin_constraints_getter
      ~Lammps.interactive_spin_constraints_setter
      ~Lammps.interactive_spins_getter
      ~Lammps.interactive_steps_getter
      ~Lammps.interactive_store_in_cache
      ~Lammps.interactive_stress_getter
      ~Lammps.interactive_structure_setter
      ~Lammps.interactive_temperatures_getter
      ~Lammps.interactive_time_getter
      ~Lammps.interactive_unwrapped_positions_getter
      ~Lammps.interactive_volume_getter
      ~Lammps.is_compressed
      ~Lammps.is_master_id
      ~Lammps.is_self_archived
      ~Lammps.iter_structures
      ~Lammps.job_file_name
      ~Lammps.kill
      ~Lammps.list_all
      ~Lammps.list_childs
      ~Lammps.list_files
      ~Lammps.list_groups
      ~Lammps.list_nodes
      ~Lammps.list_potentials
      ~Lammps.load
      ~Lammps.map
      ~Lammps.move_to
      ~Lammps.next
      ~Lammps.read_restart_file
      ~Lammps.refresh_job_status
      ~Lammps.relocate_hdf5
      ~Lammps.remap_indices
      ~Lammps.remove
      ~Lammps.remove_and_reset_id
      ~Lammps.remove_child
      ~Lammps.rename
      ~Lammps.reset_job_id
      ~Lammps.restart
      ~Lammps.run
      ~Lammps.run_if_interactive
      ~Lammps.run_if_interactive_non_modal
      ~Lammps.run_if_modal
      ~Lammps.run_if_refresh
      ~Lammps.run_if_scheduler
      ~Lammps.run_static
      ~Lammps.run_time_to_db
      ~Lammps.save
      ~Lammps.save_output
      ~Lammps.self_archive
      ~Lammps.self_unarchive
      ~Lammps.set_fix_external
      ~Lammps.set_input_to_read_only
      ~Lammps.set_potential
      ~Lammps.show_hdf
      ~Lammps.signal_intercept
      ~Lammps.species_from_hdf
      ~Lammps.store_structure
      ~Lammps.suspend
      ~Lammps.to_dict
      ~Lammps.to_hdf
      ~Lammps.to_object
      ~Lammps.trajectory
      ~Lammps.transfer_from_remote
      ~Lammps.transform_structures
      ~Lammps.update_master
      ~Lammps.update_potential
      ~Lammps.validate_ready_to_run
      ~Lammps.view_potentials
      ~Lammps.view_structure
      ~Lammps.write_input
      ~Lammps.write_restart_file
      ~Lammps.write_traj
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~Lammps.bond_dict
      ~Lammps.calculate_kwargs
      ~Lammps.child_ids
      ~Lammps.content
      ~Lammps.current_structure
      ~Lammps.cutoff_radius
      ~Lammps.database_entry
      ~Lammps.exclude_groups_hdf
      ~Lammps.exclude_nodes_hdf
      ~Lammps.executable
      ~Lammps.executor_type
      ~Lammps.files
      ~Lammps.files_to_compress
      ~Lammps.files_to_remove
      ~Lammps.id
      ~Lammps.initial_structure
      ~Lammps.interactive_enforce_structure_reset
      ~Lammps.interactive_flush_frequency
      ~Lammps.interactive_mpi_communicator
      ~Lammps.interactive_water_bonds
      ~Lammps.interactive_write_frequency
      ~Lammps.job_id
      ~Lammps.job_info_str
      ~Lammps.job_name
      ~Lammps.job_type
      ~Lammps.logger
      ~Lammps.master_id
      ~Lammps.name
      ~Lammps.number_of_structures
      ~Lammps.parent_id
      ~Lammps.path
      ~Lammps.potential
      ~Lammps.potential_available
      ~Lammps.potential_list
      ~Lammps.potential_view
      ~Lammps.project
      ~Lammps.project_hdf5
      ~Lammps.publication
      ~Lammps.queue_id
      ~Lammps.restart_file_dict
      ~Lammps.restart_file_list
      ~Lammps.server
      ~Lammps.status
      ~Lammps.structure
      ~Lammps.units
      ~Lammps.version
      ~Lammps.working_directory