atlas package
Subpackages
- atlas.active_learning package
- Subpackages
- atlas.active_learning.backends package
- atlas.active_learning.dashboard package
- atlas.active_learning.eval_test_db package
- atlas.active_learning.extrapolation package
- Submodules
- atlas.active_learning.extrapolation.autoencoder module
- atlas.active_learning.extrapolation.autoencoder_tools_aiida module
- atlas.active_learning.extrapolation.concave_hull module
- atlas.active_learning.extrapolation.morphological_closing module
- atlas.active_learning.extrapolation.quadtree module
- atlas.active_learning.extrapolation.train_autoencoder module
- Module contents
- atlas.active_learning.safeguard package
- Submodules
- atlas.active_learning.active_learning_utils module
aiida_serialized_ase_dict_to_atoms()aiida_wait_submit()calculate_fps_scores_descriptor()check_atl_ids()check_atom_in_domain()check_md_seed_agreement()convert_database_to_ase_atoms()create_mace_lammps_model()filter_dft_calcs_threshold()flush_system_memory()gather_dft_calcs_mlip()gather_dft_calcs_vasp()gen_xyz_file_from_traj()generate_descriptors()generate_descriptors_mace()generate_descriptors_soap()generate_model_name()get_dft_calc_builder_mlip_list()get_dft_calc_builder_vasp()get_final_db_path()get_model_energies_std()get_model_energies_variance()get_model_forces_std()get_model_forces_variance()get_outliers_from_calc_list()get_results_dir_path()get_species_from_database()get_total_num_frames()iqr_outlier_check()load_database()manual_progress_display()md_apply_temperature_ramp()md_coexistence_final_step_log()md_save_gen_structs()md_stop_explode_filter()md_write_frame_traj()model_res_dict_to_arr()plot_concave_hull()prepare_output_dataframe()prepare_output_final_training_db()prepare_test_set()process_call_root()read_toml_settings()remove_isolated_atoms()remove_structs_from_seed_gen_db()return_code_from_settings()run_mace_md_ase()sampler_populate_E_and_F_list()save_descriptors()select_dft_structures()select_md_frames_to_keep()select_structures_data_reduction()select_structures_fps()select_structures_lowest_energy()select_structures_random()select_structures_uncertainty()serialize_ase()simplify_forces_struct()standardize_atoms_info()suppress_stdout()update_mace_train_settings_dict()vasprun_add_info_dict()write_gathered_dft_calcs_to_file()
- atlas.active_learning.conversion module
- atlas.active_learning.mace_tools_aiida module
- atlas.active_learning.report_utils module
gather_stdout_and_scheduler()gen_al_loop_report()gen_batch_report()gen_init_db_report()gen_performance_report()generate_error_plot()generate_latent_space_evol()get_al_loop_performance()get_al_step_performance()get_latent_spaces_database_files()get_latent_spaces_workchain()get_loop_report()get_mlip_eval_results()get_ncores_from_calcjob()get_runtime_from_calcjob()mark_and_remove_outliers()output_al_stats_dict()plot_al_loop_report()plot_performance_stacked_bar()print_performance_report()simplify_timedelta_str()
- Module contents
- Subpackages
- atlas.benchmarks package
- atlas.core package
- Subpackages
- atlas.core.command_line package
- Subpackages
- Submodules
- atlas.core.command_line.cli_active_learning module
- atlas.core.command_line.cli_dashboard module
- atlas.core.command_line.cli_db_analysis module
- atlas.core.command_line.cli_generate_configuration_file module
- atlas.core.command_line.cli_generate_docs module
- atlas.core.command_line.cli_generate_init_db module
- atlas.core.command_line.cli_latent_space_analysis module
- atlas.core.command_line.cli_run_initial_config module
- atlas.core.command_line.cli_train_autoencoder module
- atlas.core.command_line.command_line_utils module
- Module contents
- atlas.core.database package
- atlas.core.filtering package
- atlas.core.gui package
- atlas.core.command_line package
- Submodules
- atlas.core.clusters module
- atlas.core.code_utils module
ATLHighlighterATLRichHandlerLevelNameFilteratl_show_progress()check_atl_version()create_handler_filters()custom_print()deprecated()display_qr_in_cli()get_atl_version_info()get_cache_path()get_config_path()get_console_handler()get_last_tagged_version()get_last_tagged_version_local()get_list_of_tags()init_cache_dir()init_config_dir()init_logger()logging_set_levels()save_qr_to_file()
- atlas.core.exceptions module
- atlas.core.initial_db module
InitialDatabaseInitialDatabase.dfInitialDatabase.database_nameInitialDatabase.database_pathInitialDatabase.max_num_atomsInitialDatabase.secretsInitialDatabase.use_offsetInitialDatabase.Ang2BohrInitialDatabase.Bohr2AngInitialDatabase.Eh2eVInitialDatabase.add_single_atoms()InitialDatabase.apply_min_deformation()InitialDatabase.apply_vacancies_random()InitialDatabase.db_struct_to_ase()InitialDatabase.descriptors_concave_hull()InitialDatabase.display_db_ase()InitialDatabase.eV2EhInitialDatabase.export_db()InitialDatabase.find_repeat_structures()InitialDatabase.gather_base_structures()InitialDatabase.gen_init_md_frames()InitialDatabase.gen_report()InitialDatabase.generate_bulk_structures()InitialDatabase.generate_clusters()InitialDatabase.generate_n2p2_input_aiida()InitialDatabase.get_base_structs_current_phase()InitialDatabase.get_db_shape()InitialDatabase.get_soap_descriptors()InitialDatabase.get_structure_list()InitialDatabase.kBInitialDatabase.limit_structure_number_phases()InitialDatabase.load_database()InitialDatabase.plot_database_composition()InitialDatabase.query_mp_api_prototype()InitialDatabase.read_base_structures()InitialDatabase.remove_structs_out_of_atom_count_range()InitialDatabase.remove_structs_out_of_cell_size_range()InitialDatabase.save_database()InitialDatabase.standardize_struct_ids()
cli_gen_db_report()cli_run_gen_initial_database()get_database_report()get_step_to_structure_mapping()get_struct_idx_from_uuid()output_db_status()report_completed_step()
- atlas.core.phase_diagram module
- atlas.core.structure module
- atlas.core.surfaces module
- atlas.core.utils module
AdsorbateAdderadd_adsorbates()apply_central_atom_octahedral()apply_filters_db()apply_gauss_perturb_db()apply_replacement()apply_replacement_no_db()check_incorrect_ratios()clear_previous_print()create_symmetrical_prototype()display_dataframe_ase()display_struct_list_ase()find_supercell_indices()fit_replacements_phase()fix_bottom_layers()gather_secrets()gauss_perturb()gen_base_elem_perc()limit_num_structures_phase()similarity_check_list()
- Module contents
- Subpackages
- atlas.training package
- atlas.workflows package
- Subpackages
- Submodules
- atlas.workflows.aiida_utils module
CalcTypeadd_aiida_group_to_db()can_submit_calculation()choose_queue()choose_queue_from_struct()determine_vacuum_direction()gather_calc_data_from_row()generate_incar()generate_kpoints_data()generate_potential_mapping()get_or_create_containerized_code()get_or_create_portable_code()get_vdw_params()kpoint_mesh_from_density()parse_stress_from_structure()run_dataframe_vasp_aiida_queue()run_dataframe_vasp_simulations_aiida()select_kspacing()sort_chunk_size()submit_aiida_vasp_calculation()update_db_with_dft_results()validate_kspacing()
- atlas.workflows.monitors module
- atlas.workflows.simple_active_learning module
SimpleActiveLearningBaseWorkChainSimpleActiveLearningBaseWorkChain.add_dft_results_to_db()SimpleActiveLearningBaseWorkChain.check_al_loop_conditions()SimpleActiveLearningBaseWorkChain.check_resume_mode()SimpleActiveLearningBaseWorkChain.compile_safeguard_model()SimpleActiveLearningBaseWorkChain.copy_input_toml_file()SimpleActiveLearningBaseWorkChain.define()SimpleActiveLearningBaseWorkChain.gather_safeguard_compiled()SimpleActiveLearningBaseWorkChain.get_al_loop_break_conditions()SimpleActiveLearningBaseWorkChain.get_data_reduction_seed()SimpleActiveLearningBaseWorkChain.get_database()SimpleActiveLearningBaseWorkChain.get_input_report()SimpleActiveLearningBaseWorkChain.get_md_seed()SimpleActiveLearningBaseWorkChain.get_results_loop()SimpleActiveLearningBaseWorkChain.get_seed_structures()SimpleActiveLearningBaseWorkChain.log_atl_version()SimpleActiveLearningBaseWorkChain.parse_safeguard_check_results()SimpleActiveLearningBaseWorkChain.results_final()SimpleActiveLearningBaseWorkChain.run_safeguard_check()SimpleActiveLearningBaseWorkChain.safeguard_check_md()SimpleActiveLearningBaseWorkChain.setup()SimpleActiveLearningBaseWorkChain.setup_textfile_logging()SimpleActiveLearningBaseWorkChain.should_run_according_to_safeguard_check()SimpleActiveLearningBaseWorkChain.should_run_safeguard()
SimpleActiveLearningWorkChainSimpleActiveLearningWorkChain.check_extrapolation_enabled()SimpleActiveLearningWorkChain.compile_models_for_inference()SimpleActiveLearningWorkChain.define()SimpleActiveLearningWorkChain.gather_compiled_models()SimpleActiveLearningWorkChain.gen_descriptors_and_concave_hull()SimpleActiveLearningWorkChain.get_descriptor_results()SimpleActiveLearningWorkChain.get_mlip_train_output()SimpleActiveLearningWorkChain.get_test_db_results()SimpleActiveLearningWorkChain.is_test_db_evaluation_enabled()SimpleActiveLearningWorkChain.perform_test_db_evaluation()SimpleActiveLearningWorkChain.return_seed_dft_and_model()SimpleActiveLearningWorkChain.run_md_seed()SimpleActiveLearningWorkChain.select_data_reduction_structures()SimpleActiveLearningWorkChain.send_calc_or_remove_structures()SimpleActiveLearningWorkChain.set_step_logger()SimpleActiveLearningWorkChain.should_select_data_reduction_structures()SimpleActiveLearningWorkChain.step_setup()SimpleActiveLearningWorkChain.train_mlip_model()
- Module contents
Module contents
Library for streamlining the structure creation and training for NNPs.