Index

A

active_learning_run_print_details() (in module atlas.core.command_line.cli_active_learning) add_phase() (atlas.core.phase_diagram.BasePhaseDiagram method) alpha_shape() (in module atlas.active_learning.extrapolation.concave_hull) apply_defaults() (in module atlas.core.command_line.command_line_utils) atl_show_progress() (in module atlas.core.code_utils) atlas module atlas.active_learning 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.core 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_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_run_initial_config module atlas.core.command_line.cli_train_autoencoder module atlas.core.command_line.command_line_utils module atlas.core.database module atlas.core.exceptions module atlas.core.phase_diagram module atlas.workflows 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 ATLHighlighter (class in atlas.core.code_utils) ATLRichHandler (class in atlas.core.code_utils) AtomNotFoundForCluster Autoencoder (class in atlas.active_learning.extrapolation.autoencoder)

B

base_style (atlas.core.code_utils.ATLHighlighter attribute) BasePhaseDiagram (class in atlas.core.phase_diagram)

BaseStructureNotFound BinaryPhaseDiagram (class in atlas.core.phase_diagram)

C

check_atl_version() (in module atlas.core.code_utils) check_atom_in_domain() (in module atlas.active_learning.extrapolation.concave_hull) 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_if_points_in_polygons() (in module atlas.active_learning.extrapolation.quadtree) check_traj_in_domain() (in module atlas.active_learning.extrapolation.concave_hull)

CompositionNotMatchingElementListError console_output() (in module atlas.core.command_line.cli_dashboard) contains() (atlas.active_learning.extrapolation.quadtree.Rectangle method) create_active_learning_builder() (in module atlas.core.command_line.cli_active_learning) create_handler_filters() (in module atlas.core.code_utils) create_image_mask() (in module atlas.active_learning.extrapolation.morphological_closing) custom_print() (in module atlas.core.code_utils)

D

decoder (atlas.active_learning.extrapolation.autoencoder.Autoencoder attribute) define() (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)

deprecated() (in module atlas.core.code_utils) display_image() (atlas.workflows.datatypes.image_types.ImagePNGData method) display_qr_in_cli() (in module atlas.core.code_utils)

E

emit() (atlas.core.code_utils.ATLRichHandler method) EmptyDataBase encoder (atlas.active_learning.extrapolation.autoencoder.Autoencoder attribute)

evaluate_dependency() (in module atlas.core.command_line.command_line_utils) evaluate_reconstruction() (in module atlas.active_learning.extrapolation.autoencoder) extract_boundaries_from_mask() (in module atlas.active_learning.extrapolation.morphological_closing)

F

fields (atlas.workflows.datatypes.mlip.MLIPModelFileData attribute) filter() (atlas.core.code_utils.LevelNameFilter method) 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) 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)

G

gen_default_config() (in module atlas.core.command_line.cli_generate_configuration_file) gen_initial_database() (in module atlas.core.command_line.cli_generate_init_db) generate_command() (in module atlas.core.command_line.cli_generate_configuration_file) generate_docs() (in module atlas.core.command_line.cli_generate_docs) generate_full_documentation() (in module atlas.core.command_line.cli_generate_docs) 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_tool_section() (in module atlas.core.command_line.cli_generate_docs) get_area() (atlas.active_learning.extrapolation.quadtree.Rectangle method) get_atl_version_info() (in module atlas.core.code_utils) get_base_elem_perc() (atlas.core.phase_diagram.Phase method) get_cache_path() (in module atlas.core.code_utils)

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_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_list_of_tags() (in module atlas.core.code_utils) get_optimized_concave_hull() (in module atlas.active_learning.extrapolation.concave_hull) get_phase() (atlas.core.phase_diagram.BasePhaseDiagram method) get_schema() (in module atlas.core.command_line.command_line_utils) GetConcaveHullCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetConcaveHullCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetLatentSpaceAutoencoderCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) GetLatentSpaceAutoencoderCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida)

H

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

highlights (atlas.core.code_utils.ATLHighlighter attribute)

I

ImagePNGData (class in atlas.workflows.datatypes.image_types) IncompatibleDataBase IncompatiblePhaseError

init_cache_dir() (in module atlas.core.code_utils) init_config_dir() (in module atlas.core.code_utils) init_logger() (in module atlas.core.code_utils) insert() (atlas.active_learning.extrapolation.quadtree.QuadTree method)

K

key_path_in_schema() (in module atlas.core.command_line.command_line_utils)

L

LevelNameFilter (class in atlas.core.code_utils) load_autoencoder_model() (in module atlas.active_learning.extrapolation.autoencoder)

load_config() (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) locate_standarization_files() (in module atlas.active_learning.extrapolation.autoencoder) logging_set_levels() (in module atlas.core.code_utils)

M

main() (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) material (atlas.core.phase_diagram.BasePhaseDiagram attribute) MissingElementError MissingMandatoryParameterError MLIPModelFileData (class in atlas.workflows.datatypes.mlip) module atlas atlas.active_learning 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.core 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_generate_configuration_file atlas.core.command_line.cli_generate_docs atlas.core.command_line.cli_generate_init_db atlas.core.command_line.cli_run_initial_config atlas.core.command_line.cli_train_autoencoder atlas.core.command_line.command_line_utils atlas.core.database atlas.core.exceptions atlas.core.phase_diagram atlas.workflows 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

monitor_al_loop() (in module atlas.core.command_line.cli_dashboard)

O

output_monitor() (in module atlas.workflows.monitors)

P

parse() (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) parse_arguments() (in module atlas.workflows.dft.vasp.aiida_run_vasp_dft_database) parse_input_toml() (in module atlas.core.command_line.command_line_utils) perc_in_phase() (atlas.core.phase_diagram.Phase method) Phase (class in atlas.core.phase_diagram) PhaseDiagram() (in module atlas.core.phase_diagram) PhaseDiagramEmpty PhaseNotFound

phases (atlas.core.phase_diagram.BasePhaseDiagram attribute) plot_concave_hull() (in module atlas.active_learning.extrapolation.concave_hull) plot_diagram() (atlas.core.phase_diagram.BinaryPhaseDiagram method) (atlas.core.phase_diagram.SinglePhaseDiagram method) (atlas.core.phase_diagram.TernaryPhaseDiagram method) prepare_cli_args_autoencoder() (in module atlas.active_learning.extrapolation.autoencoder_tools_aiida) prepare_for_submission() (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) process_morphological_closing() (in module atlas.active_learning.extrapolation.morphological_closing)

Q

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

R

read_toml_config() (in module atlas.core.command_line.cli_active_learning) Rectangle (class in atlas.active_learning.extrapolation.quadtree) resume_al_loop_builder() (in module atlas.core.command_line.cli_active_learning) return_dataset_loader() (in module atlas.active_learning.extrapolation.train_autoencoder) run_active_learning() (in module atlas.core.command_line.cli_active_learning)

run_dashboard_app() (in module atlas.core.command_line.cli_dashboard) run_gen_initial_database() (in module atlas.core.command_line.cli_generate_init_db) run_initial_config() (in module atlas.core.command_line.cli_run_initial_config) run_train_autoencoder() (in module atlas.core.command_line.cli_train_autoencoder) run_training() (in module atlas.active_learning.extrapolation.train_autoencoder)

S

safe_to_gpu() (in module atlas.active_learning.extrapolation.train_autoencoder) save_qr_to_file() (in module atlas.core.code_utils) separate_clusters() (in module atlas.active_learning.extrapolation.quadtree) setup_quadtree() (in module atlas.active_learning.extrapolation.quadtree)

should_validate_mandatory() (in module atlas.core.command_line.command_line_utils) SinglePhaseDiagram (class in atlas.core.phase_diagram) split_dataset() (in module atlas.active_learning.extrapolation.train_autoencoder) subdivide() (atlas.active_learning.extrapolation.quadtree.QuadTree method)

T

TernaryPhaseDiagram (class in atlas.core.phase_diagram) train_loop() (in module atlas.active_learning.extrapolation.train_autoencoder)

TrainAutoencoderCalculation (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida) TrainAutoencoderCalculationParser (class in atlas.active_learning.extrapolation.autoencoder_tools_aiida)

V

val_loop() (in module atlas.active_learning.extrapolation.train_autoencoder) 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_parameter() (in module atlas.core.command_line.command_line_utils) validate_section_recursive() (in module atlas.core.command_line.command_line_utils) ValidationError visualize_quadtree() (in module atlas.active_learning.extrapolation.quadtree)

W

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

wrap_text_with_rich() (in module atlas.core.command_line.cli_generate_configuration_file)

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)