pyiron\_atomistics.lammps.base.LammpsBase
=========================================

.. currentmodule:: pyiron_atomistics.lammps.base

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

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~LammpsBase.__init__
      ~LammpsBase.animate_structure
      ~LammpsBase.animate_structures
      ~LammpsBase.calc_md
      ~LammpsBase.calc_minimize
      ~LammpsBase.calc_static
      ~LammpsBase.calc_vcsgc
      ~LammpsBase.check_if_job_exists
      ~LammpsBase.check_setup
      ~LammpsBase.clear_bonds
      ~LammpsBase.clear_job
      ~LammpsBase.collect_logfiles
      ~LammpsBase.collect_output
      ~LammpsBase.collect_structures
      ~LammpsBase.compress
      ~LammpsBase.continue_with_final_structure
      ~LammpsBase.continue_with_restart_files
      ~LammpsBase.convergence_check
      ~LammpsBase.copy
      ~LammpsBase.copy_file_to_working_directory
      ~LammpsBase.copy_template
      ~LammpsBase.copy_to
      ~LammpsBase.create_job
      ~LammpsBase.create_pipeline
      ~LammpsBase.db_entry
      ~LammpsBase.decompress
      ~LammpsBase.define_bonds
      ~LammpsBase.drop_status_to_aborted
      ~LammpsBase.enable_h5md
      ~LammpsBase.from_dict
      ~LammpsBase.from_hdf
      ~LammpsBase.from_hdf_args
      ~LammpsBase.get
      ~LammpsBase.get_calculate_function
      ~LammpsBase.get_final_structure
      ~LammpsBase.get_from_table
      ~LammpsBase.get_input_parameter_dict
      ~LammpsBase.get_job_id
      ~LammpsBase.get_neighbors
      ~LammpsBase.get_neighbors_snapshots
      ~LammpsBase.get_output_parameter_dict
      ~LammpsBase.get_potentials_for_structure
      ~LammpsBase.get_structure
      ~LammpsBase.get_workdir_file
      ~LammpsBase.gui
      ~LammpsBase.inspect
      ~LammpsBase.instantiate
      ~LammpsBase.interactive_close
      ~LammpsBase.interactive_fetch
      ~LammpsBase.interactive_flush
      ~LammpsBase.is_compressed
      ~LammpsBase.is_master_id
      ~LammpsBase.is_self_archived
      ~LammpsBase.iter_structures
      ~LammpsBase.job_file_name
      ~LammpsBase.kill
      ~LammpsBase.list_all
      ~LammpsBase.list_childs
      ~LammpsBase.list_files
      ~LammpsBase.list_groups
      ~LammpsBase.list_nodes
      ~LammpsBase.list_potentials
      ~LammpsBase.load
      ~LammpsBase.map
      ~LammpsBase.move_to
      ~LammpsBase.next
      ~LammpsBase.read_restart_file
      ~LammpsBase.refresh_job_status
      ~LammpsBase.relocate_hdf5
      ~LammpsBase.remap_indices
      ~LammpsBase.remove
      ~LammpsBase.remove_and_reset_id
      ~LammpsBase.remove_child
      ~LammpsBase.rename
      ~LammpsBase.reset_job_id
      ~LammpsBase.restart
      ~LammpsBase.run
      ~LammpsBase.run_if_interactive
      ~LammpsBase.run_if_interactive_non_modal
      ~LammpsBase.run_if_modal
      ~LammpsBase.run_if_refresh
      ~LammpsBase.run_if_scheduler
      ~LammpsBase.run_static
      ~LammpsBase.run_time_to_db
      ~LammpsBase.save
      ~LammpsBase.save_output
      ~LammpsBase.self_archive
      ~LammpsBase.self_unarchive
      ~LammpsBase.set_input_to_read_only
      ~LammpsBase.set_potential
      ~LammpsBase.show_hdf
      ~LammpsBase.signal_intercept
      ~LammpsBase.store_structure
      ~LammpsBase.suspend
      ~LammpsBase.to_dict
      ~LammpsBase.to_hdf
      ~LammpsBase.to_object
      ~LammpsBase.trajectory
      ~LammpsBase.transfer_from_remote
      ~LammpsBase.transform_structures
      ~LammpsBase.update_master
      ~LammpsBase.validate_ready_to_run
      ~LammpsBase.view_potentials
      ~LammpsBase.view_structure
      ~LammpsBase.write_input
      ~LammpsBase.write_restart_file
      ~LammpsBase.write_traj
   
   

   
   
   .. rubric:: Attributes

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