Index

A

active_config() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) active_learning_run_print_details() (in module atlas.core.command_line.cli_active_learning) add_action_button() (atlas.core.gui.widgets.config_panel.ConfigPanel method) add_adsorbates() (in module atlas.core.utils) add_aiida_group_to_db() (in module atlas.workflows.aiida_utils) add_dft_results_to_db() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) add_dynamic_item() (atlas.core.gui.gui.InputFileTab method) (atlas.core.gui.widgets.schema_form.SchemaForm method) add_phase() (atlas.core.phase_diagram.BasePhaseDiagram method) add_single_atoms() (atlas.core.initial_db.InitialDatabase method) add_view() (atlas.core.gui.widgets.side_panel.SidePanel method) adjust_color_brightness() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) adjust_vacuum() (in module atlas.core.surfaces) AdsorbateAdder (class in atlas.core.utils) aiida_serialized_ase_dict_to_atoms() (in module atlas.active_learning.active_learning_utils) aiida_wait_submit() (in module atlas.active_learning.active_learning_utils) al_checked (atlas.core.gui.project.aiida_sync.SyncResult attribute) al_run_counts() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) al_updated (atlas.core.gui.project.aiida_sync.SyncResult attribute) alpha_shape() (in module atlas.active_learning.extrapolation.concave_hull) analyze_convergence() (in module atlas.benchmarks.dft.dft_benchmark_core) Ang2Bohr (atlas.active_learning.conversion.Units attribute) (atlas.core.initial_db.InitialDatabase attribute) app_icon() (in module atlas.core.gui.icons) app_theme_changed (atlas.core.gui.pages.settings.SettingsPage attribute) append() (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) ApplicationParameters (class in atlas.core.gui.app_params) (class in atlas.core.gui.gui) apply_central_atom_octahedral() (in module atlas.core.utils) apply_defaults() (in module atlas.core.command_line.command_line_utils) apply_filter_duplicate_slabs() (in module atlas.core.filtering.structure_filters) apply_filter_evaporation() (in module atlas.core.filtering.structure_filters) apply_filter_exploding_structures() (in module atlas.core.filtering.structure_filters) apply_filter_exploding_structures_distances() (in module atlas.core.filtering.structure_filters) apply_filter_layer_distance() (in module atlas.core.filtering.structure_filters) apply_filters_db() (in module atlas.core.utils) apply_gauss_perturb_db() (in module atlas.core.clusters) (in module atlas.core.utils) apply_gauss_perturb_list() (in module atlas.core.clusters) apply_migrations() (in module atlas.core.gui.project.migrations) apply_min_deformation() (atlas.core.initial_db.InitialDatabase method) apply_replacement() (in module atlas.core.utils) apply_replacement_cluster() (in module atlas.core.clusters) apply_replacement_cluster_db() (in module atlas.core.clusters) apply_replacement_no_db() (in module atlas.core.utils) apply_replacement_surface() (in module atlas.core.surfaces) apply_struct_filters_atl_db() (in module atlas.core.filtering.structure_filters) apply_theme_to_app() (in module atlas.core.gui.themes) apply_vacancies_random() (atlas.core.initial_db.InitialDatabase method) architecture (atlas.workflows.datatypes.mlip.MLIPModelFileData property) associate_steps_to_uuids() (in module atlas.core.command_line.cli_db_analysis) atl_database_to_mace_train() (in module atlas.active_learning.conversion) atl_show_progress() (in module atlas.core.code_utils) atlas module atlas.active_learning module atlas.active_learning.active_learning_utils module atlas.active_learning.backends module atlas.active_learning.backends._base module atlas.active_learning.backends.mace module atlas.active_learning.backends.mace.calcjobs module atlas.active_learning.backends.mace.calculator module atlas.active_learning.backends.mace.descriptors module atlas.active_learning.backends.mace.training module atlas.active_learning.conversion module atlas.active_learning.dashboard module atlas.active_learning.dashboard.training_dashboard_flask module atlas.active_learning.eval_test_db module atlas.active_learning.eval_test_db.eval_test_db module atlas.active_learning.extrapolation module 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 atlas.active_learning.mace_tools_aiida module atlas.active_learning.md module atlas.active_learning.md.ase_calculators module atlas.active_learning.md.atl_process_structure module atlas.active_learning.md.md_utils module atlas.active_learning.report_utils module atlas.active_learning.safeguard module atlas.active_learning.safeguard.safeguard_utils module atlas.benchmarks module atlas.benchmarks.benchmark_utils module atlas.benchmarks.dft module atlas.benchmarks.dft.dft_benchmark_core module atlas.benchmarks.dft.dft_benchmark_report module atlas.benchmarks.dft.run_dft_benchmark module atlas.benchmarks.mlip module atlas.benchmarks.mlip.evaluate_mlip_performance module atlas.benchmarks.mlip.mlip_benchmark_utils module atlas.benchmarks.mlip.mlip_benchmarks module atlas.core module atlas.core.clusters module atlas.core.code_utils module atlas.core.command_line module 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 atlas.core.command_line.setup module atlas.core.command_line.setup._code module atlas.core.command_line.setup._common module atlas.core.command_line.setup._computer module atlas.core.command_line.setup._mpkey module atlas.core.command_line.setup._potcar module atlas.core.command_line.setup._profile module atlas.core.command_line.setup._status module atlas.core.database module atlas.core.database.diversity_metrics module atlas.core.exceptions module atlas.core.filtering module atlas.core.filtering.structure_filters module atlas.core.gui module atlas.core.gui.app_params module atlas.core.gui.gui module atlas.core.gui.hub module atlas.core.gui.icons module atlas.core.gui.pages module atlas.core.gui.pages.base module atlas.core.gui.pages.dft module atlas.core.gui.pages.dft_benchmark module atlas.core.gui.pages.logs module atlas.core.gui.pages.overview module atlas.core.gui.pages.reports module atlas.core.gui.pages.settings module atlas.core.gui.process module atlas.core.gui.process.runner module atlas.core.gui.project module atlas.core.gui.project.aiida_sync module atlas.core.gui.project.migrations module atlas.core.gui.project.project module atlas.core.gui.project.recent module atlas.core.gui.project.schema module atlas.core.gui.themes module atlas.core.gui.widgets module atlas.core.gui.widgets.aiida_suggestions module atlas.core.gui.widgets.collapsible_log_panel module atlas.core.gui.widgets.config_panel module atlas.core.gui.widgets.db_manage_panel module atlas.core.gui.widgets.dict_widgets module atlas.core.gui.widgets.latent_space_gallery module atlas.core.gui.widgets.periodic_table_widget module atlas.core.gui.widgets.phase_card_panel module atlas.core.gui.widgets.preflight_panel module atlas.core.gui.widgets.prereq_banner module atlas.core.gui.widgets.schema_form module atlas.core.gui.widgets.setup_wizard module atlas.core.gui.widgets.side_panel module atlas.core.gui.widgets.toml_editor module atlas.core.gui.widgets.validation_dialog module atlas.core.gui.widgets.workflow_view module atlas.core.initial_db module atlas.core.phase_diagram module atlas.core.structure module atlas.core.surfaces module atlas.core.utils module atlas.training module atlas.workflows module atlas.workflows.aiida_utils module atlas.workflows.datatypes module atlas.workflows.datatypes.image_types module atlas.workflows.datatypes.mlip module atlas.workflows.dft module atlas.workflows.dft.vasp module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database module atlas.workflows.monitors module atlas.workflows.simple_active_learning module ATLHighlighter (class in atlas.core.code_utils) ATLRichHandler (class in atlas.core.code_utils) ATLSafeCalculatorWrapper (class in atlas.active_learning.md.ase_calculators) AtomNotFoundForCluster Autoencoder (class in atlas.active_learning.extrapolation.autoencoder) AutoencoderSettings (class in atlas.active_learning.extrapolation.autoencoder) available_sections() (atlas.core.gui.widgets.schema_form.SchemaForm method)

B

background (atlas.core.gui.themes.Theme attribute) base_style (atlas.core.code_utils.ATLHighlighter attribute) BasePhaseDiagram (class in atlas.core.phase_diagram) BaseStructureNotFound batch_size (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) bias_flag (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) BinaryPhaseDiagram (class in atlas.core.phase_diagram) Bohr2Ang (atlas.active_learning.conversion.Units attribute) (atlas.core.initial_db.InitialDatabase attribute)

bottleneck_dim (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) bottom_structure() (in module atlas.core.clusters) build_benchmark_calculations() (in module atlas.benchmarks.dft.dft_benchmark_core) build_static_stylesheet() (in module atlas.core.gui.themes) build_stylesheet() (in module atlas.core.gui.themes) build_theme_palette() (in module atlas.core.gui.themes) Bulk (class in atlas.core.structure)

C

c01 (atlas.core.gui.themes.Theme attribute) c02 (atlas.core.gui.themes.Theme attribute) c03 (atlas.core.gui.themes.Theme attribute) c04 (atlas.core.gui.themes.Theme attribute) c05 (atlas.core.gui.themes.Theme attribute) c06 (atlas.core.gui.themes.Theme attribute) c07 (atlas.core.gui.themes.Theme attribute) c08 (atlas.core.gui.themes.Theme attribute) c09 (atlas.core.gui.themes.Theme attribute) c10 (atlas.core.gui.themes.Theme attribute) c11 (atlas.core.gui.themes.Theme attribute) c12 (atlas.core.gui.themes.Theme attribute) c13 (atlas.core.gui.themes.Theme attribute) c14 (atlas.core.gui.themes.Theme attribute) c15 (atlas.core.gui.themes.Theme attribute) c16 (atlas.core.gui.themes.Theme attribute) calcjob_entry_point (atlas.active_learning.backends._base.MLIPTrainer property) (atlas.active_learning.backends.mace.MACEBackend property) (atlas.active_learning.backends.MLIPTrainer property) CalcType (class in atlas.workflows.aiida_utils) calculate() (atlas.active_learning.md.ase_calculators.ATLSafeCalculatorWrapper method) calculate_fps_scores_descriptor() (in module atlas.active_learning.active_learning_utils) can_submit_calculation() (in module atlas.workflows.aiida_utils) category (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) center_structure() (in module atlas.core.clusters) Check (class in atlas.core.gui.widgets.preflight_panel) check_aiida() (in module atlas.core.command_line.setup._common) check_al_loop_conditions() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) check_atl_ids() (in module atlas.active_learning.active_learning_utils) check_atl_version() (in module atlas.core.code_utils) check_atom_in_domain() (in module atlas.active_learning.active_learning_utils) (in module atlas.active_learning.extrapolation.concave_hull) check_configuration() (atlas.core.gui.gui.InputFileTab method) check_correct_vacuum_size() (in module atlas.core.surfaces) check_deprecated_keys() (in module atlas.core.command_line.command_line_utils) check_deprecated_parameters() (in module atlas.core.command_line.command_line_utils) check_disconn_neighbors() (in module atlas.core.filtering.structure_filters) check_extrapolation_enabled() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) check_if_points_in_polygons() (in module atlas.active_learning.extrapolation.quadtree) check_incorrect_ratios() (in module atlas.core.utils) check_md_seed_agreement() (in module atlas.active_learning.active_learning_utils) check_resume_mode() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) check_setup_problems() (in module atlas.core.gui.widgets.setup_wizard) check_traj_in_domain() (in module atlas.active_learning.extrapolation.concave_hull) (in module atlas.active_learning.md.atl_process_structure) CheckMACECommiteeResultsCalculationParser (class in atlas.active_learning.backends.mace.calcjobs) CheckMACECommitteeResultsCalculation (class in atlas.active_learning.backends.mace.calcjobs) choose_queue() (in module atlas.workflows.aiida_utils) choose_queue_from_struct() (in module atlas.workflows.aiida_utils) clear() (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) (atlas.core.gui.widgets.schema_form.SchemaForm method) clear_highlight() (atlas.core.gui.widgets.toml_editor.TomlEditor method) clear_model_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) clear_plot_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) clear_previous_print() (in module atlas.core.utils) clear_structures_index() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) cli_gen_db_report() (in module atlas.core.initial_db) cli_run_gen_initial_database() (in module atlas.core.initial_db) close() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) Cluster (class in atlas.core.structure)

coexistence_structure_melting_point() (in module atlas.benchmarks.mlip.mlip_benchmarks) CoexistenceMDTemperatureLogger (class in atlas.active_learning.md.md_utils) CollapsibleLogPanel (class in atlas.core.gui.widgets.collapsible_log_panel) collect_data() (atlas.core.gui.widgets.config_panel.ConfigPanel method) (atlas.core.gui.widgets.phase_card_panel.PhaseCardPanel method) (atlas.core.gui.widgets.schema_form.SchemaForm method) collected_data() (atlas.core.gui.widgets.phase_card_panel.PhaseEditDialog method) compile_model() (atlas.active_learning.backends._base.MLIPModelCompiler method) (atlas.active_learning.backends.MLIPModelCompiler method) compile_models_for_inference() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) compile_safeguard_model() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) compiled_model_extension (atlas.active_learning.backends._base.MLIPModelCompiler property) (atlas.active_learning.backends.MLIPModelCompiler property) complete_benchmark() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) CompositionNotMatchingElementListError compute_area_difference() (in module atlas.core.command_line.cli_db_analysis) compute_area_growth_ratio() (in module atlas.core.command_line.cli_db_analysis) compute_heuristic_sigma() (in module atlas.core.database.diversity_metrics) compute_kpt_density() (in module atlas.benchmarks.benchmark_utils) compute_vendi_score() (in module atlas.core.command_line.cli_db_analysis) config_key (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) config_path() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) ConfigPanel (class in atlas.core.gui.widgets.config_panel) console_output() (in module atlas.core.command_line.cli_dashboard) contains() (atlas.active_learning.extrapolation.quadtree.Rectangle method) convert_database_to_ase_atoms() (in module atlas.active_learning.active_learning_utils) copy_input_toml_file() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) cosine_distance() (in module atlas.core.database.diversity_metrics) create() (atlas.core.gui.project.Project class method) (atlas.core.gui.project.project.Project class method) create_active_learning_builder() (in module atlas.core.command_line.cli_active_learning) create_args_from_toml() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) create_cache() (in module atlas.active_learning.dashboard.training_dashboard_flask) create_calculator() (atlas.active_learning.backends._base.MLIPCalculatorFactory method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPCalculatorFactory method) create_calculator_for_model() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) create_final_multi_panel_plot() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) create_foundation_model_calculator() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) create_foundation_model_paths() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) create_handler_filters() (in module atlas.core.code_utils) create_image_mask() (in module atlas.active_learning.extrapolation.morphological_closing) create_lammps_potential() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) create_layout() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) create_log_panel() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) create_mace_calculator() (in module atlas.active_learning.backends.mace.calculator) create_mace_lammps_model() (in module atlas.active_learning.active_learning_utils) create_mace_lammps_model_impl() (in module atlas.active_learning.backends.mace.training) create_progress_panel() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) create_sidebar_panel() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) create_symmetrical_prototype() (in module atlas.core.utils) current_section() (atlas.core.gui.widgets.schema_form.SchemaForm method) current_toml() (atlas.core.gui.widgets.config_panel.ConfigPanel method) current_view() (atlas.core.gui.widgets.side_panel.SidePanel method) cursor (atlas.core.gui.themes.Theme attribute) custom_print() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) (in module atlas.core.code_utils) cwd() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method)

D

database_name (atlas.core.initial_db.InitialDatabase attribute) database_path (atlas.core.initial_db.InitialDatabase attribute) dataset (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) db_struct_to_ase() (atlas.core.initial_db.InitialDatabase method) DbManagePanel (class in atlas.core.gui.widgets.db_manage_panel) decoder (atlas.active_learning.extrapolation.autoencoder.Autoencoder attribute) DEFAULT (atlas.workflows.aiida_utils.CalcType attribute) define() (atlas.active_learning.backends.mace.calcjobs.CheckMACECommitteeResultsCalculation class method) (atlas.active_learning.backends.mace.calcjobs.EvaluateMACEConfigsCalculation class method) (atlas.active_learning.backends.mace.calcjobs.GetMACEDescriptorsCalculation class method) (atlas.active_learning.backends.mace.calcjobs.TrainMACEModelCalculation class method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetConcaveHullCalculation class method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetLatentSpaceAutoencoderCalculation class method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.TrainAutoencoderCalculation class method) (atlas.active_learning.mace_tools_aiida.EvalTestDatabaseCalculation class method) (atlas.active_learning.mace_tools_aiida.GetDescriptorsCombinedCalculation class method) (atlas.active_learning.mace_tools_aiida.ProcessMDSeedStructCalculation class method) (atlas.active_learning.safeguard.safeguard_utils.RunMDSafeguardCalculation class method) (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain class method) (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain class method) define_allowed_stages() (in module atlas.active_learning.md.atl_process_structure) deprecated() (in module atlas.core.code_utils) description (atlas.core.gui.widgets.preflight_panel.Check attribute) (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) descriptors_concave_hull() (atlas.core.initial_db.InitialDatabase method) DetachedProcessMonitor (class in atlas.core.gui.process.runner)

determine_reference_value() (in module atlas.benchmarks.dft.dft_benchmark_core) determine_vacuum_direction() (in module atlas.workflows.aiida_utils) device (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) df (atlas.core.initial_db.InitialDatabase attribute) dft_checked (atlas.core.gui.project.aiida_sync.SyncResult attribute) dft_run_counts() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) dft_updated (atlas.core.gui.project.aiida_sync.SyncResult attribute) DftBenchmarkPage (class in atlas.core.gui.pages.dft_benchmark) DftPage (class in atlas.core.gui.pages.dft) dir (atlas.core.gui.project.Project property) (atlas.core.gui.project.project.Project property) display_dataframe_ase() (in module atlas.core.utils) display_db_ase() (atlas.core.initial_db.InitialDatabase method) display_image() (atlas.workflows.datatypes.image_types.ImagePNGData method) DISPLAY_NAME (atlas.core.gui.pages.base.WorkflowPage attribute) (atlas.core.gui.pages.dft.DftPage attribute) (atlas.core.gui.pages.dft_benchmark.DftBenchmarkPage attribute) (atlas.core.gui.pages.logs.LogsPage attribute) (atlas.core.gui.pages.overview.OverviewPage attribute) (atlas.core.gui.pages.reports.ReportsPage attribute) (atlas.core.gui.pages.settings.SettingsPage attribute) display_qr_in_cli() (in module atlas.core.code_utils) display_struct_list_ase() (in module atlas.core.utils) dragEnterEvent() (atlas.core.gui.widgets.config_panel.ConfigPanel method) dropEvent() (atlas.core.gui.widgets.config_panel.ConfigPanel method) dtype (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute)

E

Eh2eV (atlas.active_learning.conversion.Units attribute) (atlas.core.initial_db.InitialDatabase attribute) ElementPickerField (class in atlas.core.gui.widgets.periodic_table_widget) elements() (atlas.core.gui.widgets.periodic_table_widget.ElementPickerField method) elements_changed (atlas.core.gui.widgets.periodic_table_widget.ElementPickerField attribute) emit() (atlas.core.code_utils.ATLRichHandler method) EmptyDataBase encoder (atlas.active_learning.extrapolation.autoencoder.Autoencoder attribute) ensure_arrow_svgs() (in module atlas.core.gui.icons) errors (atlas.core.gui.project.aiida_sync.SyncResult attribute) estimated_count (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) eV2Eh (atlas.active_learning.conversion.Units attribute) (atlas.core.initial_db.InitialDatabase attribute)

EvalTestDatabaseCalculation (class in atlas.active_learning.mace_tools_aiida) EvalTestDatabaseCalculationParser (class in atlas.active_learning.mace_tools_aiida) evaluate_committee() (atlas.active_learning.backends._base.MLIPCommitteeEvaluator method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPCommitteeEvaluator method) evaluate_dependency() (in module atlas.core.command_line.command_line_utils) evaluate_reconstruction() (in module atlas.active_learning.extrapolation.autoencoder) EvaluateMACEConfigsCalculation (class in atlas.active_learning.backends.mace.calcjobs) EvaluateMACEConfigsCalculationParser (class in atlas.active_learning.backends.mace.calcjobs) eventFilter() (atlas.core.gui.gui.InputFileTab method) (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) (atlas.core.gui.widgets.schema_form.SchemaForm method) export_db() (atlas.core.initial_db.InitialDatabase method) extract_boundaries_from_mask() (in module atlas.active_learning.extrapolation.morphological_closing)

F

failing_summary() (atlas.core.gui.widgets.preflight_panel.PreflightPanel method) fetch_aiida_suggestions() (in module atlas.core.gui.widgets.aiida_suggestions) fetch_aiida_suggestions_async() (in module atlas.core.gui.widgets.aiida_suggestions) field_focused (atlas.core.gui.widgets.schema_form.SchemaForm attribute) field_key (atlas.core.gui.widgets.preflight_panel.Check attribute) fields (atlas.workflows.datatypes.mlip.MLIPModelFileData attribute) filter() (atlas.core.code_utils.LevelNameFilter method) filter_dft_calcs_threshold() (in module atlas.active_learning.active_learning_utils) filter_points_by_mask() (in module atlas.active_learning.extrapolation.morphological_closing) FilterError find_dense_leaves() (atlas.active_learning.extrapolation.quadtree.QuadTree method) find_dense_leaves_density() (atlas.active_learning.extrapolation.quadtree.QuadTree method) find_detached_process() (in module atlas.core.gui.process.runner) find_inference_model() (in module atlas.active_learning.backends) find_repeat_structures() (atlas.core.initial_db.InitialDatabase method) find_supercell_indices() (in module atlas.core.utils)

fit_replacements_phase() (in module atlas.core.utils) fix_bottom_layers() (in module atlas.core.utils) flush_system_memory() (in module atlas.active_learning.active_learning_utils) focus_field() (atlas.core.gui.widgets.config_panel.ConfigPanel method) FONT_FAMILIES_MONOSPACE (atlas.core.gui.app_params.ApplicationParameters attribute) (atlas.core.gui.gui.ApplicationParameters attribute) FONT_FAMILIES_REGULAR (atlas.core.gui.app_params.ApplicationParameters attribute) (atlas.core.gui.gui.ApplicationParameters attribute) foreground (atlas.core.gui.themes.Theme attribute) format_parameter_line() (in module atlas.core.command_line.cli_generate_docs) format_value() (in module atlas.core.command_line.cli_generate_configuration_file) forward() (atlas.active_learning.extrapolation.autoencoder.Autoencoder method) FoundationModelPath (class in atlas.benchmarks.mlip.mlip_benchmark_utils) from_ase_atoms() (atlas.core.structure.Structure class method) from_db_row() (atlas.core.structure.Structure method) from_string() (atlas.workflows.aiida_utils.CalcType class method) from_vasprun() (atlas.core.structure.Structure method)

G

gather_base_structures() (atlas.core.initial_db.InitialDatabase method) gather_calc_data_from_node() (in module atlas.active_learning.conversion) gather_calc_data_from_row() (in module atlas.workflows.aiida_utils) gather_compiled_models() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) gather_dft_calcs_mlip() (in module atlas.active_learning.active_learning_utils) gather_dft_calcs_vasp() (in module atlas.active_learning.active_learning_utils) gather_information() (in module atlas.active_learning.dashboard.training_dashboard_flask) gather_safeguard_compiled() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) gather_secrets() (in module atlas.core.utils) gather_stdout_and_scheduler() (in module atlas.active_learning.report_utils) gauss_perturb() (in module atlas.core.utils) gen_al_loop_report() (in module atlas.active_learning.report_utils) gen_base_elem_perc() (in module atlas.core.utils) gen_batch_report() (in module atlas.active_learning.report_utils) gen_default_config() (in module atlas.core.command_line.cli_generate_configuration_file) gen_descriptors_and_concave_hull() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) gen_init_db_report() (in module atlas.active_learning.report_utils) gen_init_md_frames() (atlas.core.initial_db.InitialDatabase method) gen_initial_database() (in module atlas.core.command_line.cli_generate_init_db) gen_kspacing_from_vasp_input() (in module atlas.benchmarks.benchmark_utils) gen_mace_train_aiida() (in module atlas.active_learning.conversion) gen_mace_train_structure_list() (in module atlas.active_learning.conversion) gen_magic_number_list_chini() (in module atlas.benchmarks.mlip.mlip_benchmarks) gen_n2p2_train_aiida() (in module atlas.active_learning.conversion) gen_perc_surfaces() (in module atlas.core.surfaces) gen_performance_report() (in module atlas.active_learning.report_utils) gen_report() (atlas.core.initial_db.InitialDatabase method) gen_surfaces_diff_miller_parallel() (in module atlas.core.surfaces) gen_xyz_file_from_traj() (in module atlas.active_learning.active_learning_utils) generate_bulk_structures() (atlas.core.initial_db.InitialDatabase method) generate_clusters() (atlas.core.initial_db.InitialDatabase method) generate_command() (in module atlas.core.command_line.cli_generate_configuration_file) generate_descriptors() (atlas.active_learning.backends._base.MLIPDescriptorProvider method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPDescriptorProvider method) (in module atlas.active_learning.active_learning_utils) generate_descriptors_mace() (in module atlas.active_learning.active_learning_utils) (in module atlas.active_learning.backends.mace.descriptors) generate_descriptors_soap() (in module atlas.active_learning.active_learning_utils) generate_docs() (in module atlas.core.command_line.cli_generate_docs) generate_error_plot() (in module atlas.active_learning.report_utils) generate_full_documentation() (in module atlas.core.command_line.cli_generate_docs) generate_full_report() (in module atlas.benchmarks.dft.dft_benchmark_report) generate_incar() (in module atlas.workflows.aiida_utils) generate_kpoints_data() (in module atlas.workflows.aiida_utils) generate_latent_space_evol() (in module atlas.active_learning.report_utils) generate_model_name() (in module atlas.active_learning.active_learning_utils) generate_n2p2_input_aiida() (atlas.core.initial_db.InitialDatabase method) generate_potential_mapping() (in module atlas.workflows.aiida_utils) generate_section_docs() (in module atlas.core.command_line.cli_generate_docs) generate_template() (in module atlas.core.command_line.cli_generate_configuration_file) generate_toml_recursive() (in module atlas.core.command_line.cli_generate_configuration_file) generate_toml_snippet() (in module atlas.benchmarks.dft.dft_benchmark_core) generate_tool_section() (in module atlas.core.command_line.cli_generate_docs) get_al_loop_break_conditions() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_al_loop_performance() (in module atlas.active_learning.report_utils) get_al_step_performance() (in module atlas.active_learning.report_utils) get_area() (atlas.active_learning.extrapolation.quadtree.Rectangle method) get_atl_version_info() (in module atlas.core.code_utils) get_available_filters() (in module atlas.core.filtering.structure_filters) get_backend() (in module atlas.active_learning.backends) get_base_elem_perc() (atlas.core.phase_diagram.Phase method) get_base_structs_current_phase() (atlas.core.initial_db.InitialDatabase method) get_cache_path() (in module atlas.core.code_utils) get_center_of_mass() (in module atlas.core.clusters) get_circles_metric_db() (in module atlas.core.database.diversity_metrics) get_complete_steps_uuid() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_concave_hull_python() (in module atlas.active_learning.extrapolation.concave_hull) get_config_path() (in module atlas.core.code_utils) get_console_handler() (in module atlas.core.code_utils) get_coord_nums() (in module atlas.core.filtering.structure_filters) get_data_reduction_seed() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_database() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method)

get_database_report() (in module atlas.core.initial_db) get_db_shape() (atlas.core.initial_db.InitialDatabase method) get_descriptor_results() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) get_dft_calc_builder_mlip_list() (in module atlas.active_learning.active_learning_utils) get_dft_calc_builder_vasp() (in module atlas.active_learning.active_learning_utils) get_element_constants() (in module atlas.core.clusters) get_feature_matrix_with_custom_features() (in module atlas.core.database.diversity_metrics) get_final_db_path() (in module atlas.active_learning.active_learning_utils) get_input_report() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_last_tagged_version() (in module atlas.core.code_utils) get_last_tagged_version_local() (in module atlas.core.code_utils) get_latent_space_autoencoder() (in module atlas.active_learning.extrapolation.autoencoder) get_latent_spaces_database_files() (in module atlas.active_learning.report_utils) get_latent_spaces_workchain() (in module atlas.active_learning.report_utils) get_list_of_tags() (in module atlas.core.code_utils) get_loop_report() (in module atlas.active_learning.report_utils) get_max_layer_distance() (in module atlas.core.filtering.structure_filters) get_md_seed() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_miller_index_str() (in module atlas.core.surfaces) get_missing_cache_steps_uuid() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_mlip_eval_results() (in module atlas.active_learning.report_utils) get_mlip_train_output() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) get_model_color() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_model_colors_by_names() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_model_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_model_display_name() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_model_display_names() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_model_energies_std() (in module atlas.active_learning.active_learning_utils) get_model_energies_variance() (in module atlas.active_learning.active_learning_utils) get_model_forces_std() (in module atlas.active_learning.active_learning_utils) get_model_forces_variance() (in module atlas.active_learning.active_learning_utils) get_model_stats() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_ncores_from_calcjob() (in module atlas.active_learning.report_utils) get_optimized_concave_hull() (in module atlas.active_learning.extrapolation.concave_hull) get_or_create_containerized_code() (in module atlas.workflows.aiida_utils) get_or_create_portable_code() (in module atlas.workflows.aiida_utils) get_outliers_from_calc_list() (in module atlas.active_learning.active_learning_utils) get_phase() (atlas.core.phase_diagram.BasePhaseDiagram method) get_plot_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_progbar_class_name() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_property() (atlas.active_learning.md.ase_calculators.ATLSafeCalculatorWrapper method) get_report() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_results_dir_path() (in module atlas.active_learning.active_learning_utils) get_results_loop() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_runtime_from_calcjob() (in module atlas.active_learning.report_utils) get_schema() (in module atlas.core.command_line.command_line_utils) get_seed_structures() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) get_soap_descriptors() (atlas.core.initial_db.InitialDatabase method) get_species_from_database() (in module atlas.active_learning.active_learning_utils) get_step_child_info() (in module atlas.active_learning.dashboard.training_dashboard_flask) get_step_to_structure_mapping() (in module atlas.core.initial_db) get_struct_idx_from_uuid() (in module atlas.core.initial_db) get_struct_type() (in module atlas.active_learning.conversion) get_structure_list() (atlas.core.initial_db.InitialDatabase method) get_test_db_results() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) get_total_num_frames() (in module atlas.active_learning.active_learning_utils) get_ui_manager() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) get_value() (atlas.core.gui.widgets.dict_widgets.IncarWidget method) (atlas.core.gui.widgets.dict_widgets.KspacingWidget method) get_vdw_params() (in module atlas.workflows.aiida_utils) get_vendi_score() (in module atlas.core.database.diversity_metrics) get_vendi_score_db_rbf() (in module atlas.core.database.diversity_metrics) get_vendi_score_db_simple() (in module atlas.core.database.diversity_metrics) get_vendi_score_subsampling() (in module atlas.core.database.diversity_metrics) GetConcaveHullCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetConcaveHullCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetDescriptorsCombinedCalculation (class in atlas.active_learning.mace_tools_aiida) GetDescriptorsCombinedParser (class in atlas.active_learning.mace_tools_aiida) GetLatentSpaceAutoencoderCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetLatentSpaceAutoencoderCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetMACEDescriptorsCalculation (class in atlas.active_learning.backends.mace.calcjobs) GetMACEDescriptorsCalculationParser (class in atlas.active_learning.backends.mace.calcjobs) group (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute)

H

h (atlas.active_learning.extrapolation.quadtree.Rectangle attribute) has_errors (atlas.core.gui.widgets.preflight_panel.PreflightPanel property) heading() (in module atlas.core.command_line.setup._common) hide_view() (atlas.core.gui.widgets.side_panel.SidePanel method)

highlight_path() (atlas.core.gui.widgets.toml_editor.TomlEditor method) highlightBlock() (atlas.core.gui.gui.TomlHighlighter method) (atlas.core.gui.widgets.toml_editor.TomlHighlighter method) highlights (atlas.core.code_utils.ATLHighlighter attribute) HubDialog (class in atlas.core.gui.hub)

I

ImagePNGData (class in atlas.workflows.datatypes.image_types) implemented_properties (atlas.active_learning.md.ase_calculators.ATLSafeCalculatorWrapper attribute) IncarWidget (class in atlas.core.gui.widgets.dict_widgets) IncompatibleDataBase IncompatiblePhaseError init_cache_dir() (in module atlas.core.code_utils) init_config_dir() (in module atlas.core.code_utils) init_db_name() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) init_db_path() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) init_logger() (in module atlas.core.code_utils)

InitialDatabase (class in atlas.core.initial_db) initialise() (in module atlas.core.gui.project.schema) initialize_model_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) InputFileTab (class in atlas.core.gui.gui) insert() (atlas.active_learning.extrapolation.quadtree.QuadTree method) invalidate_aiida_suggestions_cache() (in module atlas.core.gui.widgets.aiida_suggestions) iqr_outlier_check() (in module atlas.active_learning.active_learning_utils) is_active (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) is_exposed() (atlas.core.utils.AdsorbateAdder method) is_filter (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) is_test_db_evaluation_enabled() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) IsolatedAtom (class in atlas.core.structure) iter_leaf_widgets() (atlas.core.gui.widgets.schema_form.SchemaForm method)

K

kB (atlas.active_learning.conversion.Units attribute) (atlas.core.initial_db.InitialDatabase attribute)

key_path_in_schema() (in module atlas.core.command_line.command_line_utils) kpoint_mesh_from_density() (in module atlas.workflows.aiida_utils) KspacingWidget (class in atlas.core.gui.widgets.dict_widgets)

L

l1_hidden_dim (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) l2_hidden_dim (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) label (atlas.core.gui.widgets.preflight_panel.Check attribute) lammps_pair_style (atlas.active_learning.backends._base.MLIPCalculatorFactory property) (atlas.active_learning.backends.mace.MACEBackend property) (atlas.active_learning.backends.MLIPCalculatorFactory property) LAMMPSMACERawParser (class in atlas.active_learning.backends.mace.calcjobs) last_opened_at (atlas.core.gui.project.recent.RecentEntry attribute) last_opened_when (atlas.core.gui.project.recent.RecentEntry property) LatentSpaceGallery (class in atlas.core.gui.widgets.latent_space_gallery) latest_al_run_id() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) LauncherDialog (class in atlas.core.gui.gui) LevelNameFilter (class in atlas.core.code_utils) limit_md_frames() (in module atlas.active_learning.md.atl_process_structure) limit_num_structures_phase() (in module atlas.core.utils) limit_structure_number_phases() (atlas.core.initial_db.InitialDatabase method) list_al_iterations() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) list_al_runs() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) list_backends() (in module atlas.active_learning.backends) list_codes() (in module atlas.core.command_line.setup._common) list_computers() (in module atlas.core.command_line.setup._common) list_config_snapshots() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) list_dft_runs() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) list_inference_models() (in module atlas.active_learning.backends) list_profiles() (in module atlas.core.command_line.setup._common)

list_structures() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) load_and_save_descriptors() (in module atlas.core.database.diversity_metrics) load_autoencoder_model() (in module atlas.active_learning.extrapolation.autoencoder) load_config() (in module atlas.benchmarks.dft.run_dft_benchmark) (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) load_data() (atlas.core.gui.widgets.config_panel.ConfigPanel method) load_database() (atlas.core.initial_db.InitialDatabase class method) (in module atlas.active_learning.active_learning_utils) load_model (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) load_model() (atlas.workflows.datatypes.mlip.MLIPModelFileData method) load_model_from_aiida() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) load_schema() (atlas.core.gui.gui.InputFileTab method) (atlas.core.gui.widgets.schema_form.SchemaForm method) load_toml_config() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) load_toml_from_dialog() (atlas.core.gui.gui.InputFileTab method) (atlas.core.gui.widgets.config_panel.ConfigPanel method) locate_standarization_files() (in module atlas.active_learning.extrapolation.autoencoder) log() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) (atlas.core.gui.gui.MainWindow method) log_atl_version() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) log_message (atlas.core.gui.gui.ProcessWorker attribute) (atlas.core.gui.process.runner.DetachedProcessMonitor attribute) (atlas.core.gui.process.runner.ProcessRunner attribute) log_path() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) logging_set_levels() (in module atlas.core.code_utils) LogsPage (class in atlas.core.gui.pages.logs) loss (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) lr (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute)

M

MACEBackend (class in atlas.active_learning.backends.mace) main() (in module atlas.benchmarks.dft.run_dft_benchmark) (in module atlas.benchmarks.mlip.evaluate_mlip_performance) (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) MainWindow (class in atlas.core.gui.gui) make_clean_cluster() (in module atlas.core.clusters) make_clean_dimer() (in module atlas.core.clusters) manual_progress_display() (in module atlas.active_learning.active_learning_utils) mark_and_remove_outliers() (in module atlas.active_learning.report_utils) material (atlas.core.phase_diagram.BasePhaseDiagram attribute) max_num_atoms (atlas.core.initial_db.InitialDatabase attribute) md_apply_temperature_ramp() (in module atlas.active_learning.active_learning_utils) md_coexistence_final_step_log() (in module atlas.active_learning.active_learning_utils) md_save_gen_structs() (in module atlas.active_learning.active_learning_utils) md_stop_explode_filter() (in module atlas.active_learning.active_learning_utils) md_write_frame_traj() (in module atlas.active_learning.active_learning_utils) meta() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) MissingElementError MissingMandatoryParameterError MLIPCalculatorFactory (class in atlas.active_learning.backends) (class in atlas.active_learning.backends._base) MLIPCommitteeEvaluator (class in atlas.active_learning.backends) (class in atlas.active_learning.backends._base) MLIPDescriptorProvider (class in atlas.active_learning.backends) (class in atlas.active_learning.backends._base) MLIPModelCompiler (class in atlas.active_learning.backends) (class in atlas.active_learning.backends._base) MLIPModelFileData (class in atlas.workflows.datatypes.mlip) MLIPTrainer (class in atlas.active_learning.backends) (class in atlas.active_learning.backends._base) model_file_ext() (in module atlas.active_learning.backends) model_file_extension (atlas.active_learning.backends._base.MLIPCalculatorFactory property) (atlas.active_learning.backends.mace.MACEBackend property) (atlas.active_learning.backends.MLIPCalculatorFactory property) model_file_stem() (in module atlas.active_learning.backends) model_path (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) model_res_dict_to_arr() (in module atlas.active_learning.active_learning_utils) modifications_breakdown() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) module atlas atlas.active_learning atlas.active_learning.active_learning_utils atlas.active_learning.backends atlas.active_learning.backends._base atlas.active_learning.backends.mace atlas.active_learning.backends.mace.calcjobs atlas.active_learning.backends.mace.calculator atlas.active_learning.backends.mace.descriptors atlas.active_learning.backends.mace.training atlas.active_learning.conversion atlas.active_learning.dashboard atlas.active_learning.dashboard.training_dashboard_flask atlas.active_learning.eval_test_db atlas.active_learning.eval_test_db.eval_test_db atlas.active_learning.extrapolation atlas.active_learning.extrapolation.autoencoder atlas.active_learning.extrapolation.autoencoder_tools_aiida atlas.active_learning.extrapolation.concave_hull atlas.active_learning.extrapolation.morphological_closing atlas.active_learning.extrapolation.quadtree atlas.active_learning.extrapolation.train_autoencoder atlas.active_learning.mace_tools_aiida atlas.active_learning.md atlas.active_learning.md.ase_calculators atlas.active_learning.md.atl_process_structure atlas.active_learning.md.md_utils atlas.active_learning.report_utils atlas.active_learning.safeguard atlas.active_learning.safeguard.safeguard_utils atlas.benchmarks atlas.benchmarks.benchmark_utils atlas.benchmarks.dft atlas.benchmarks.dft.dft_benchmark_core atlas.benchmarks.dft.dft_benchmark_report atlas.benchmarks.dft.run_dft_benchmark atlas.benchmarks.mlip atlas.benchmarks.mlip.evaluate_mlip_performance atlas.benchmarks.mlip.mlip_benchmark_utils atlas.benchmarks.mlip.mlip_benchmarks atlas.core atlas.core.clusters atlas.core.code_utils atlas.core.command_line atlas.core.command_line.cli_active_learning atlas.core.command_line.cli_dashboard atlas.core.command_line.cli_db_analysis atlas.core.command_line.cli_generate_configuration_file atlas.core.command_line.cli_generate_docs atlas.core.command_line.cli_generate_init_db atlas.core.command_line.cli_latent_space_analysis atlas.core.command_line.cli_run_initial_config atlas.core.command_line.cli_train_autoencoder atlas.core.command_line.command_line_utils atlas.core.command_line.setup atlas.core.command_line.setup._code atlas.core.command_line.setup._common atlas.core.command_line.setup._computer atlas.core.command_line.setup._mpkey atlas.core.command_line.setup._potcar atlas.core.command_line.setup._profile atlas.core.command_line.setup._status atlas.core.database atlas.core.database.diversity_metrics atlas.core.exceptions atlas.core.filtering atlas.core.filtering.structure_filters atlas.core.gui atlas.core.gui.app_params atlas.core.gui.gui atlas.core.gui.hub atlas.core.gui.icons atlas.core.gui.pages atlas.core.gui.pages.base atlas.core.gui.pages.dft atlas.core.gui.pages.dft_benchmark atlas.core.gui.pages.logs atlas.core.gui.pages.overview atlas.core.gui.pages.reports atlas.core.gui.pages.settings atlas.core.gui.process atlas.core.gui.process.runner atlas.core.gui.project atlas.core.gui.project.aiida_sync atlas.core.gui.project.migrations atlas.core.gui.project.project atlas.core.gui.project.recent atlas.core.gui.project.schema atlas.core.gui.themes atlas.core.gui.widgets atlas.core.gui.widgets.aiida_suggestions atlas.core.gui.widgets.collapsible_log_panel atlas.core.gui.widgets.config_panel atlas.core.gui.widgets.db_manage_panel atlas.core.gui.widgets.dict_widgets atlas.core.gui.widgets.latent_space_gallery atlas.core.gui.widgets.periodic_table_widget atlas.core.gui.widgets.phase_card_panel atlas.core.gui.widgets.preflight_panel atlas.core.gui.widgets.prereq_banner atlas.core.gui.widgets.schema_form atlas.core.gui.widgets.setup_wizard atlas.core.gui.widgets.side_panel atlas.core.gui.widgets.toml_editor atlas.core.gui.widgets.validation_dialog atlas.core.gui.widgets.workflow_view atlas.core.initial_db atlas.core.phase_diagram atlas.core.structure atlas.core.surfaces atlas.core.utils atlas.training atlas.workflows atlas.workflows.aiida_utils atlas.workflows.datatypes atlas.workflows.datatypes.image_types atlas.workflows.datatypes.mlip atlas.workflows.dft atlas.workflows.dft.vasp atlas.workflows.dft.vasp.aiida_run_vasp_dft_database atlas.workflows.monitors atlas.workflows.simple_active_learning

monitor_al_loop() (in module atlas.core.command_line.cli_dashboard) monitor_and_collect() (in module atlas.benchmarks.dft.dft_benchmark_core)

N

n_atoms_list() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) name (atlas.core.gui.project.Project property) (atlas.core.gui.project.project.Project property) (atlas.core.gui.project.recent.RecentEntry attribute) (atlas.core.gui.themes.Theme attribute) (atlas.core.gui.widgets.workflow_view.WorkflowStep attribute) NAVIGATION_KEY (atlas.core.gui.pages.base.WorkflowPage attribute) (atlas.core.gui.pages.dft.DftPage attribute) (atlas.core.gui.pages.dft_benchmark.DftBenchmarkPage attribute) (atlas.core.gui.pages.logs.LogsPage attribute) (atlas.core.gui.pages.overview.OverviewPage attribute) (atlas.core.gui.pages.reports.ReportsPage attribute) (atlas.core.gui.pages.settings.SettingsPage attribute)

needs_first_run_wizard() (in module atlas.core.gui.widgets.setup_wizard) NewProjectDialog (class in atlas.core.gui.hub) num_epochs (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute)

O

on_process_finished() (atlas.core.gui.gui.MainWindow method) on_schema_selected() (atlas.core.gui.gui.InputFileTab method) on_shown() (atlas.core.gui.pages.base.WorkflowPage method) (atlas.core.gui.pages.dft.DftPage method) (atlas.core.gui.pages.dft_benchmark.DftBenchmarkPage method) (atlas.core.gui.pages.overview.OverviewPage method) (atlas.core.gui.pages.reports.ReportsPage method) (atlas.core.gui.pages.settings.SettingsPage method)

on_toml_text_changed() (atlas.core.gui.gui.InputFileTab method) open() (atlas.core.gui.project.Project class method) (atlas.core.gui.project.project.Project class method) output_al_stats_dict() (in module atlas.active_learning.report_utils) output_db_status() (in module atlas.core.initial_db) output_monitor() (in module atlas.workflows.monitors) OverviewPage (class in atlas.core.gui.pages.overview)

P

parse() (atlas.active_learning.backends.mace.calcjobs.CheckMACECommiteeResultsCalculationParser method) (atlas.active_learning.backends.mace.calcjobs.EvaluateMACEConfigsCalculationParser method) (atlas.active_learning.backends.mace.calcjobs.GetMACEDescriptorsCalculationParser method) (atlas.active_learning.backends.mace.calcjobs.LAMMPSMACERawParser method) (atlas.active_learning.backends.mace.calcjobs.TrainMACEModelCalculationParser method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetConcaveHullCalculationParser method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetLatentSpaceAutoencoderCalculationParser method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.TrainAutoencoderCalculationParser method) (atlas.active_learning.mace_tools_aiida.EvalTestDatabaseCalculationParser method), [1] (atlas.active_learning.mace_tools_aiida.GetDescriptorsCombinedParser method), [1] (atlas.active_learning.mace_tools_aiida.ProcessMDSeedStructCalculationParser method) (atlas.active_learning.safeguard.safeguard_utils.RunMDSafeguardCalculationParser method) parse_args() (in module atlas.core.command_line.cli_db_analysis) parse_arguments() (in module atlas.benchmarks.dft.run_dft_benchmark) (in module atlas.benchmarks.mlip.mlip_benchmark_utils) (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) parse_input_toml() (in module atlas.core.command_line.command_line_utils) parse_safeguard_check_results() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) parse_stress_from_structure() (in module atlas.workflows.aiida_utils) parse_training_results() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) parsed_config() (atlas.core.gui.widgets.config_panel.ConfigPanel method) parser_entry_point (atlas.active_learning.backends._base.MLIPTrainer property) (atlas.active_learning.backends.mace.MACEBackend property) (atlas.active_learning.backends.MLIPTrainer property) path (atlas.core.gui.project.recent.RecentEntry attribute) patience (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) perc_in_phase() (atlas.core.phase_diagram.Phase method) perform_test_db_evaluation() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) PeriodicTableDialog (class in atlas.core.gui.widgets.periodic_table_widget) Phase (class in atlas.core.phase_diagram) phase_count() (atlas.core.gui.widgets.phase_card_panel.PhaseCardPanel method) PhaseCardPanel (class in atlas.core.gui.widgets.phase_card_panel) PhaseDiagram() (in module atlas.core.phase_diagram) PhaseDiagramEmpty PhaseEditDialog (class in atlas.core.gui.widgets.phase_card_panel) PhaseNotFound phases (atlas.core.phase_diagram.BasePhaseDiagram attribute) pid_file (atlas.core.gui.process.runner.ProcessRunner property) plain_text() (atlas.core.gui.widgets.toml_editor.TomlEditor method) plot_al_loop_report() (in module atlas.active_learning.report_utils) plot_concave_hull() (in module atlas.active_learning.active_learning_utils) (in module atlas.active_learning.extrapolation.concave_hull) plot_convergence() (in module atlas.benchmarks.dft.dft_benchmark_report) plot_database_composition() (atlas.core.initial_db.InitialDatabase method) plot_diagram() (atlas.core.phase_diagram.BinaryPhaseDiagram method) (atlas.core.phase_diagram.SinglePhaseDiagram method) (atlas.core.phase_diagram.TernaryPhaseDiagram method) plot_performance_stacked_bar() (in module atlas.active_learning.report_utils)

populate() (atlas.core.gui.widgets.phase_card_panel.PhaseCardPanel method) populate_from_data() (atlas.core.gui.widgets.schema_form.SchemaForm method) populate_suggestions() (atlas.core.gui.widgets.config_panel.ConfigPanel method) (atlas.core.gui.widgets.schema_form.SchemaForm method) PreflightPanel (class in atlas.core.gui.widgets.preflight_panel) prepare_builder() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) prepare_cli_args_autoencoder() (in module atlas.active_learning.extrapolation.autoencoder_tools_aiida) prepare_cli_args_mace() (in module atlas.active_learning.backends.mace.calcjobs) prepare_coexistence_structure_lammps() (in module atlas.benchmarks.mlip.mlip_benchmarks) prepare_for_submission() (atlas.active_learning.backends.mace.calcjobs.CheckMACECommitteeResultsCalculation method) (atlas.active_learning.backends.mace.calcjobs.EvaluateMACEConfigsCalculation method) (atlas.active_learning.backends.mace.calcjobs.GetMACEDescriptorsCalculation method) (atlas.active_learning.backends.mace.calcjobs.RunMDCalculationGPULAMMPS method) (atlas.active_learning.backends.mace.calcjobs.TrainMACEModelCalculation method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetConcaveHullCalculation method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.GetLatentSpaceAutoencoderCalculation method) (atlas.active_learning.extrapolation.autoencoder_tools_aiida.TrainAutoencoderCalculation method) (atlas.active_learning.mace_tools_aiida.EvalTestDatabaseCalculation method) (atlas.active_learning.mace_tools_aiida.GetDescriptorsCombinedCalculation method) (atlas.active_learning.mace_tools_aiida.ProcessMDSeedStructCalculation method) (atlas.active_learning.safeguard.safeguard_utils.RunMDSafeguardCalculation method) prepare_output_dataframe() (in module atlas.active_learning.active_learning_utils) prepare_output_final_training_db() (in module atlas.active_learning.active_learning_utils) prepare_test_set() (in module atlas.active_learning.active_learning_utils) prepare_training_data() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) PrereqBanner (class in atlas.core.gui.widgets.prereq_banner) pretty_label() (in module atlas.core.gui.app_params) print_performance_report() (in module atlas.active_learning.report_utils) print_summary_table() (in module atlas.benchmarks.dft.dft_benchmark_report) process_call_root() (in module atlas.active_learning.active_learning_utils) process_data_boundaries() (in module atlas.core.command_line.cli_db_analysis) process_finished (atlas.core.gui.gui.ProcessWorker attribute) (atlas.core.gui.process.runner.DetachedProcessMonitor attribute) (atlas.core.gui.process.runner.ProcessRunner attribute) process_morphological_closing() (in module atlas.active_learning.extrapolation.morphological_closing) process_row_parallel() (in module atlas.core.surfaces) process_running_changed (atlas.core.gui.pages.base.WorkflowPage attribute) ProcessMDSeedStructCalculation (class in atlas.active_learning.mace_tools_aiida) ProcessMDSeedStructCalculationParser (class in atlas.active_learning.mace_tools_aiida) ProcessRunner (class in atlas.core.gui.process.runner) ProcessWorker (class in atlas.core.gui.gui) Project (class in atlas.core.gui.project) (class in atlas.core.gui.project.project) ProjectError, [1] prune_missing() (atlas.core.gui.project.recent.RecentProjects method) (atlas.core.gui.project.RecentProjects method)

Q

QuadTree (class in atlas.active_learning.extrapolation.quadtree)

query_mp_api_prototype() (atlas.core.initial_db.InitialDatabase method)

R

read_base_structures() (atlas.core.initial_db.InitialDatabase method) read_schema_version() (in module atlas.core.gui.project.schema) read_toml_config() (in module atlas.core.command_line.cli_active_learning) read_toml_settings() (in module atlas.active_learning.active_learning_utils) RecentEntry (class in atlas.core.gui.project.recent) RecentProjects (class in atlas.core.gui.project) (class in atlas.core.gui.project.recent) record_al_submission() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) record_dft_submission() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) Rectangle (class in atlas.active_learning.extrapolation.quadtree) refresh() (atlas.core.gui.pages.overview.OverviewPage method) (atlas.core.gui.widgets.db_manage_panel.DbManagePanel method) (atlas.core.gui.widgets.latent_space_gallery.LatentSpaceGallery method) (atlas.core.gui.widgets.setup_wizard.SetupStatusPanel method) refresh_al_run() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) refresh_dft_runs() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) refresh_structures_index() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) refresh_toml_preview() (atlas.core.gui.widgets.config_panel.ConfigPanel method) register_backend() (in module atlas.active_learning.backends) RELAX_BULK (atlas.workflows.aiida_utils.CalcType attribute) RELAX_CLUSTER (atlas.workflows.aiida_utils.CalcType attribute) RELAX_SURFACE (atlas.workflows.aiida_utils.CalcType attribute) remove() (atlas.core.gui.project.recent.RecentProjects method) (atlas.core.gui.project.RecentProjects method) remove_isolated_atoms() (in module atlas.active_learning.active_learning_utils) remove_structs_from_seed_gen_db() (in module atlas.active_learning.active_learning_utils) remove_structs_out_of_atom_count_range() (atlas.core.initial_db.InitialDatabase method) remove_structs_out_of_cell_size_range() (atlas.core.initial_db.InitialDatabase method) remove_structures_from_index() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) report_completed_step() (in module atlas.core.initial_db) ReportsPage (class in atlas.core.gui.pages.reports) require_profile() (in module atlas.core.command_line.setup._common) requires_aiida (atlas.core.gui.widgets.preflight_panel.Check attribute) restyle() (atlas.core.gui.widgets.prereq_banner.PrereqBanner method) (atlas.core.gui.widgets.prereq_banner.SuccessBanner method) results_final() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) resume_al_loop_builder() (in module atlas.core.command_line.cli_active_learning) return_code_from_settings() (in module atlas.active_learning.active_learning_utils) return_dataset_loader() (in module atlas.active_learning.extrapolation.train_autoencoder)

return_seed_dft_and_model() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) RichUIManager (class in atlas.benchmarks.mlip.mlip_benchmark_utils) rng_seed (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) run (atlas.core.gui.widgets.preflight_panel.Check attribute) run() (atlas.core.gui.gui.ProcessWorker method) (atlas.core.gui.pages.dft.DftPage method) (atlas.core.gui.pages.dft_benchmark.DftBenchmarkPage method) (atlas.core.gui.process.runner.DetachedProcessMonitor method) (atlas.core.gui.process.runner.ProcessRunner method) run_active_learning() (in module atlas.core.command_line.cli_active_learning) run_checks() (atlas.core.gui.widgets.preflight_panel.PreflightPanel method) run_dashboard_app() (in module atlas.core.command_line.cli_dashboard) run_database_analysis() (in module atlas.core.command_line.cli_db_analysis) run_dataframe_vasp_aiida_queue() (in module atlas.workflows.aiida_utils) run_dataframe_vasp_simulations_aiida() (in module atlas.workflows.aiida_utils) run_defect_formation_energy_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_elastic_properties_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_energy_md_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_evaluate_database() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_final_db_size_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_gen_initial_database() (in module atlas.core.command_line.cli_generate_init_db) run_gsfe_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_high_temp_md_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_initial_config() (in module atlas.core.command_line.cli_run_initial_config) run_latent_space_analysis() (in module atlas.core.command_line.cli_latent_space_analysis) run_learning_curves_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_mace_md_ase() (in module atlas.active_learning.active_learning_utils) run_magic_cluster_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_md_count_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_md_seed() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) run_melting_point_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_phonon_dispersion_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_process() (atlas.core.gui.gui.InputFileTab method) run_safeguard_check() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) run_surface_energies_benchmark() (in module atlas.benchmarks.mlip.mlip_benchmarks) run_train_autoencoder() (in module atlas.core.command_line.cli_train_autoencoder) run_training() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) (in module atlas.active_learning.extrapolation.train_autoencoder) run_training_dashboard() (in module atlas.active_learning.dashboard.training_dashboard_flask) RunMDCalculationGPULAMMPS (class in atlas.active_learning.backends.mace.calcjobs) RunMDCalculationGPULAMMPSMACE (in module atlas.active_learning.backends.mace.calcjobs) RunMDSafeguardCalculation (class in atlas.active_learning.safeguard.safeguard_utils) RunMDSafeguardCalculationParser (class in atlas.active_learning.safeguard.safeguard_utils)

S

safe_to_gpu() (in module atlas.active_learning.extrapolation.train_autoencoder) safeguard_check_md() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) sampler_populate_E_and_F_list() (in module atlas.active_learning.active_learning_utils) save_config_snapshot() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) save_database() (atlas.core.initial_db.InitialDatabase method) save_descriptors() (in module atlas.active_learning.active_learning_utils) save_global_toml_theme() (in module atlas.core.gui.themes) save_plot_dual_format() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) save_qr_to_file() (in module atlas.core.code_utils) save_to_db() (atlas.core.structure.Structure method) save_to_file() (atlas.core.gui.gui.InputFileTab method) (atlas.core.gui.widgets.config_panel.ConfigPanel method) save_to_project() (atlas.core.gui.widgets.config_panel.ConfigPanel method) saved_global_theme() (in module atlas.core.gui.themes) saved_global_toml_theme() (in module atlas.core.gui.themes) schema_loaded (atlas.core.gui.widgets.schema_form.SchemaForm attribute) SchemaForm (class in atlas.core.gui.widgets.schema_form) secrets (atlas.core.initial_db.InitialDatabase attribute) section_changed (atlas.core.gui.widgets.schema_form.SchemaForm attribute) section_key (atlas.core.gui.widgets.config_panel.ConfigPanel property) select_best_model() (atlas.active_learning.backends._base.MLIPTrainer method) (atlas.active_learning.backends.mace.MACEBackend method) (atlas.active_learning.backends.MLIPTrainer method) select_data_reduction_structures() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) select_dft_structures() (in module atlas.active_learning.active_learning_utils) select_kspacing() (in module atlas.workflows.aiida_utils) select_md_frames_to_keep() (in module atlas.active_learning.active_learning_utils) select_representative_structures() (in module atlas.benchmarks.dft.dft_benchmark_core) select_structures_data_reduction() (in module atlas.active_learning.active_learning_utils) select_structures_fps() (in module atlas.active_learning.active_learning_utils) select_structures_lowest_energy() (in module atlas.active_learning.active_learning_utils) select_structures_random() (in module atlas.active_learning.active_learning_utils) select_structures_uncertainty() (in module atlas.active_learning.active_learning_utils) selected_elements() (atlas.core.gui.widgets.periodic_table_widget.PeriodicTableDialog method) send_calc_or_remove_structures() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) separate_clusters() (in module atlas.active_learning.extrapolation.quadtree) serialize_ase() (in module atlas.active_learning.active_learning_utils) set_app_theme() (atlas.core.gui.pages.base.WorkflowPage method) (atlas.core.gui.widgets.config_panel.ConfigPanel method) set_current_section() (atlas.core.gui.widgets.schema_form.SchemaForm method) set_current_view() (atlas.core.gui.widgets.side_panel.SidePanel method) set_elements() (atlas.core.gui.widgets.periodic_table_widget.ElementPickerField method) set_highlighter_theme() (atlas.core.gui.gui.InputFileTab method) set_message() (atlas.core.gui.widgets.prereq_banner.PrereqBanner method) (atlas.core.gui.widgets.prereq_banner.SuccessBanner method) set_meta() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) set_model_display_name() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) set_plot_data() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) set_schema() (atlas.core.gui.widgets.schema_form.SchemaForm method) set_step_logger() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) set_steps() (atlas.core.gui.widgets.workflow_view.WorkflowView method) set_suggestions_loading() (atlas.core.gui.widgets.config_panel.ConfigPanel method) (atlas.core.gui.widgets.schema_form.SchemaForm method) set_text() (atlas.core.gui.widgets.toml_editor.TomlEditor method) set_theme() (atlas.core.gui.pages.base.WorkflowPage method) (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) (atlas.core.gui.widgets.config_panel.ConfigPanel method) (atlas.core.gui.widgets.side_panel.SidePanel method) (atlas.core.gui.widgets.toml_editor.TomlEditor method) (atlas.core.gui.widgets.workflow_view.WorkflowView method) set_ui_manager() (in module atlas.benchmarks.mlip.mlip_benchmark_utils) set_value() (atlas.core.gui.widgets.dict_widgets.IncarWidget method) (atlas.core.gui.widgets.dict_widgets.KspacingWidget method) set_workflow_steps() (atlas.core.gui.widgets.config_panel.ConfigPanel method) setText() (atlas.core.gui.widgets.periodic_table_widget.ElementPickerField method)

SettingsPage (class in atlas.core.gui.pages.settings) setUp() (atlas.core.database.diversity_metrics.TestVendiScore method) setup() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) setup_code() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._code) setup_computer() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._computer) setup_mp_key() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._mpkey) setup_potcar() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._potcar) setup_profile() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._profile) setup_quadtree() (in module atlas.active_learning.extrapolation.quadtree) setup_textfile_logging() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) SetupStatusPanel (class in atlas.core.gui.widgets.setup_wizard) SetupWizard (class in atlas.core.gui.widgets.setup_wizard) should_run_according_to_safeguard_check() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) should_run_safeguard() (atlas.workflows.simple_active_learning.SimpleActiveLearningBaseWorkChain method) should_select_data_reduction_structures() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) should_validate_mandatory() (in module atlas.core.command_line.command_line_utils) show_status() (in module atlas.core.command_line.setup) (in module atlas.core.command_line.setup._status) show_view() (atlas.core.gui.widgets.side_panel.SidePanel method) showEvent() (atlas.core.gui.widgets.side_panel.SidePanel method) SidePanel (class in atlas.core.gui.widgets.side_panel) similarity_check_list() (in module atlas.core.utils) simple_extrapolation_check() (in module atlas.active_learning.md.atl_process_structure) SimpleActiveLearningBaseWorkChain (class in atlas.workflows.simple_active_learning) SimpleActiveLearningWorkChain (class in atlas.workflows.simple_active_learning) simplify_forces_struct() (in module atlas.active_learning.active_learning_utils) simplify_timedelta_str() (in module atlas.active_learning.report_utils) SinglePhaseDiagram (class in atlas.core.phase_diagram) slab_to_bottom() (in module atlas.core.surfaces) sort_chunk_size() (in module atlas.workflows.aiida_utils) SP_BULK (atlas.workflows.aiida_utils.CalcType attribute) SP_CLUSTER (atlas.workflows.aiida_utils.CalcType attribute) SP_ISOLATEDATOM (atlas.workflows.aiida_utils.CalcType attribute) SP_SURFACE (atlas.workflows.aiida_utils.CalcType attribute) split_dataset() (in module atlas.active_learning.extrapolation.train_autoencoder) standardize_atoms_info() (in module atlas.active_learning.active_learning_utils) standardize_data (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) standardize_struct_ids() (atlas.core.initial_db.InitialDatabase method) start_benchmark() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) step_clicked (atlas.core.gui.widgets.workflow_view.WorkflowView attribute) step_setup() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) stop() (atlas.core.gui.gui.ProcessWorker method) (atlas.core.gui.process.runner.DetachedProcessMonitor method) (atlas.core.gui.process.runner.ProcessRunner method) Structure (class in atlas.core.structure) structure_breakdown() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) structure_counts() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) subdivide() (atlas.active_learning.extrapolation.quadtree.QuadTree method) submit_aiida_vasp_calculation() (in module atlas.workflows.aiida_utils) submit_benchmark_calculations() (in module atlas.benchmarks.dft.dft_benchmark_core) SuccessBanner (class in atlas.core.gui.widgets.prereq_banner) summary (atlas.core.gui.project.aiida_sync.SyncResult property) supports_committee_training (atlas.active_learning.backends._base.MLIPCommitteeEvaluator property) (atlas.active_learning.backends.mace.MACEBackend property) (atlas.active_learning.backends.MLIPCommitteeEvaluator property) suppress_stdout() (in module atlas.active_learning.active_learning_utils) Surface (class in atlas.core.structure) sync_al_runs() (in module atlas.core.gui.project.aiida_sync) sync_all() (in module atlas.core.gui.project.aiida_sync) sync_dft_runs() (in module atlas.core.gui.project.aiida_sync) SyncResult (class in atlas.core.gui.project.aiida_sync)

T

tanimoto_distance() (in module atlas.core.database.diversity_metrics) tearDown() (atlas.core.database.diversity_metrics.TestVendiScore method) terminate_process() (atlas.core.gui.process.runner.DetachedProcessMonitor method) TernaryPhaseDiagram (class in atlas.core.phase_diagram) test_frac (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) test_identical_modes() (atlas.core.database.diversity_metrics.TestVendiScore method) test_orthogonal_modes() (atlas.core.database.diversity_metrics.TestVendiScore method) test_shape_and_color_overlap() (atlas.core.database.diversity_metrics.TestVendiScore method) test_two_distinct_groups() (atlas.core.database.diversity_metrics.TestVendiScore method) TestVendiScore (class in atlas.core.database.diversity_metrics) text() (atlas.core.gui.widgets.periodic_table_widget.ElementPickerField method) Theme (class in atlas.core.gui.themes) theme_changed (atlas.core.gui.pages.settings.SettingsPage attribute) theme_colors() (in module atlas.core.gui.themes) theme_names() (in module atlas.core.gui.themes) theme_variant() (in module atlas.core.gui.themes) themed_icon() (in module atlas.core.gui.icons) THEMES (atlas.core.gui.gui.TomlHighlighter attribute) (atlas.core.gui.widgets.toml_editor.TomlHighlighter attribute)

to_ase_atoms() (atlas.core.structure.Structure method) to_bulk() (atlas.core.structure.Structure method) to_cluster() (atlas.core.structure.Structure method) to_surface() (atlas.core.structure.Structure method) toggle() (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) toggled (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel attribute) TomlEditor (class in atlas.core.gui.widgets.toml_editor) TomlHighlighter (class in atlas.core.gui.gui) (class in atlas.core.gui.widgets.toml_editor) touch() (atlas.core.gui.project.recent.RecentProjects method) (atlas.core.gui.project.RecentProjects method) train_frac (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) train_loop() (in module atlas.active_learning.extrapolation.train_autoencoder) train_mlip_model() (atlas.workflows.simple_active_learning.SimpleActiveLearningWorkChain method) TrainAutoencoderCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) TrainAutoencoderCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) TrainMACEModelCalculation (class in atlas.active_learning.backends.mace.calcjobs) TrainMACEModelCalculationParser (class in atlas.active_learning.backends.mace.calcjobs) tray_icon() (in module atlas.core.gui.icons)

U

Units (class in atlas.active_learning.conversion) UnphysicalStateError unread_count_changed (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel attribute) update_al_run_status() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) update_cache() (in module atlas.active_learning.dashboard.training_dashboard_flask) update_db_with_dft_results() (in module atlas.workflows.aiida_utils)

update_display() (atlas.benchmarks.mlip.mlip_benchmark_utils.RichUIManager method) update_mace_train_settings_dict() (in module atlas.active_learning.active_learning_utils) (in module atlas.active_learning.backends.mace.training) update_toml_preview() (atlas.core.gui.gui.InputFileTab method) upsert_al_iterations() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method) use_offset (atlas.core.initial_db.InitialDatabase attribute)

V

val_loop() (in module atlas.active_learning.extrapolation.train_autoencoder) valid_frac (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) validate_command() (in module atlas.core.command_line.cli_generate_configuration_file) validate_config_file() (in module atlas.core.command_line.command_line_utils) validate_current() (atlas.core.gui.widgets.config_panel.ConfigPanel method) validate_kspacing() (in module atlas.workflows.aiida_utils) validate_parameter() (in module atlas.core.command_line.command_line_utils) validate_section_recursive() (in module atlas.core.command_line.command_line_utils)

validated (atlas.core.gui.widgets.config_panel.ConfigPanel attribute) ValidationDialog (class in atlas.core.gui.widgets.validation_dialog) ValidationError variant (atlas.core.gui.themes.Theme attribute) vasprun_add_info_dict() (in module atlas.active_learning.active_learning_utils) view_changed (atlas.core.gui.widgets.side_panel.SidePanel attribute) viewer() (atlas.core.gui.widgets.collapsible_log_panel.CollapsibleLogPanel method) visualize_quadtree() (in module atlas.active_learning.extrapolation.quadtree)

W

w (atlas.active_learning.extrapolation.quadtree.Rectangle attribute) wandb (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) wandb_name (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) wandb_project (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) weight_decay (atlas.active_learning.extrapolation.autoencoder.AutoencoderSettings attribute) workflow_state() (atlas.core.gui.project.Project method) (atlas.core.gui.project.project.Project method)

workflow_step_clicked (atlas.core.gui.widgets.config_panel.ConfigPanel attribute) WorkflowPage (class in atlas.core.gui.pages.base) WorkflowStep (class in atlas.core.gui.widgets.workflow_view) WorkflowView (class in atlas.core.gui.widgets.workflow_view) wrap_text_with_rich() (in module atlas.core.command_line.cli_generate_configuration_file) write_gathered_dft_calcs_to_file() (in module atlas.active_learning.active_learning_utils)

X

x (atlas.active_learning.extrapolation.quadtree.Rectangle attribute)

xmax (atlas.active_learning.extrapolation.quadtree.Rectangle property) xmin (atlas.active_learning.extrapolation.quadtree.Rectangle property)

Y

y (atlas.active_learning.extrapolation.quadtree.Rectangle attribute)

ymax (atlas.active_learning.extrapolation.quadtree.Rectangle property) ymin (atlas.active_learning.extrapolation.quadtree.Rectangle property)