Index

A

ACSDAnalyzer (class in mala.network.acsd_analyzer) add_hyperparameter() (ACSDAnalyzer method) (HyperOpt method) (HyperOptOAT method) add_snapshot() (ACSDAnalyzer method) (DataConverter method) (DataHandlerBase method) (DataShuffler method) (LDOSAligner method)

add_snapshot_to_dataset() (LazyLoadDataset method) after_training_metric (ParametersRunning property) align_ldos_to_ref() (LDOSAligner method) allocate_shared_mem() (LazyLoadDatasetSingle method) analytical_integration() (in module mala.targets.calculation_helpers) assume_two_dimensional (ParametersTargets attribute) atomic_density_sigma (ParametersDescriptors attribute) AtomicDensity (class in mala.descriptors.atomic_density) AtomicForce (class in mala.targets.atomic_force)

B

backconvert_units() (AtomicDensity static method) (Bispectrum static method) (Density static method) (Descriptor static method) (DOS static method) (LDOS static method) (MinterpyDescriptors static method) (Target static method)

band_energy (DOS property) (LDOS property) barrier() (in module mala.common.parallelizer) bidirection (ParametersNetwork attribute) Bispectrum (class in mala.descriptors.bispectrum) bispectrum_cutoff (ParametersDescriptors property) bispectrum_switchflag (ParametersDescriptors property) bispectrum_twojmax (ParametersDescriptors attribute)

C

calc_optimal_ldos_shift() (LDOSAligner static method) calculate() (MALA method) calculate_from_atoms() (Descriptor method) calculate_from_qe_out() (Descriptor method) calculate_loss() (Network method) calculate_properties() (MALA method) check_modules() (in module mala.common.check_modules) checkpoint_exists() (HyperOpt class method) checkpoint_name (ParametersRunning attribute) checkpoints_each_epoch (ParametersRunning attribute) cleanup() (MultiLazyLoadDataLoader method) clear_data() (DataHandler method) (DataHandlerBase method)

clear_hyperparameters() (HyperOpt method) comment (Parameters attribute) convert_local_to_3d() (Descriptor method) convert_snapshots() (DataConverter method) convert_units() (AtomicDensity static method) (AtomicForce static method) (Bispectrum static method) (Density static method) (Descriptor static method) (DOS static method) (LDOS static method) (MinterpyDescriptors static method) (Target static method) CubeFile (class in mala.targets.cube_parser)

D

data (Parameters attribute) data_name (AtomicDensity property) (Bispectrum property) (Density property) (DOS property) (LDOS property) (MinterpyDescriptors property) (PhysicalData property) data_splitting_type (ParametersData attribute) DataConverter (class in mala.datahandling.data_converter) DataHandler (class in mala.datahandling.data_handler) DataHandlerBase (class in mala.datahandling.data_handler_base) DataScaler (class in mala.datahandling.data_scaler) DataShuffler (class in mala.datahandling.data_shuffler) deallocate_shared_mem() (LazyLoadDatasetSingle method) delete_data() (LazyLoadDatasetSingle method)

Density (class in mala.targets.density) density (Density property) (LDOS property) density_of_states (DOS property) (LDOS property) Descriptor (class in mala.descriptors.descriptor) descriptor_calculator (DataConverter attribute) descriptor_type (ParametersDescriptors attribute) descriptors (Parameters attribute) descriptors_contain_xyz (Descriptor property) (ParametersDescriptors attribute) device (Parameters property) direction (ParametersHyperparameterOptimization attribute) do_prediction() (Network method) DOS (class in mala.targets.dos) during_training_metric (ParametersRunning property)

E

early_stopping_epochs (ParametersRunning attribute) early_stopping_threshold (ParametersRunning attribute) energy_grid (DOS property) (LDOS property)

enforce_pbc() (Descriptor static method) entropy_contribution (DOS property) (LDOS property) entropy_multiplicator() (in module mala.targets.calculation_helpers) extract_compute_np() (in module mala.descriptors.lammps_utils)

F

FastTensorDataset (class in mala.datahandling.fast_tensor_dataset) feature_size (AtomicDensity property) (Bispectrum property) (Density property) (DOS property) (LDOS property) (MinterpyDescriptors property) (PhysicalData property) (Target property) FeedForwardNet (class in mala.network.network) fermi_energy (DOS property) (LDOS property) fermi_function() (in module mala.targets.calculation_helpers) finalize() (in module mala.common.parallelizer) finish_incremental_fitting() (DataScaler method) first_snapshot (TrajectoryAnalyzer property) fit() (DataScaler method) forward() (FeedForwardNet method) (GRU method) (LSTM method) (Network method) (PositionalEncoding method) (TransformerNet method)

from_cube_file() (Density class method) (LDOS class method) from_json() (JSONSerializable class method) (ParametersBase class method) (Snapshot class method) from_ldos_calculator() (Density class method) (DOS class method) from_numpy_array() (Density class method) (DOS class method) (LDOS class method) from_numpy_file() (Density class method) (DOS class method) (LDOS class method) from_openpmd_file() (Density class method) (LDOS class method) from_qe_dos_txt() (DOS class method) from_qe_out() (DOS class method) from_xsf_file() (Density class method) (LDOS class method)

G

gather_descriptors() (Descriptor method) gaussians() (in module mala.targets.calculation_helpers) generate_square_subsequent_mask() (TransformerNet static method) get_atomic_forces() (Density method) (LDOS method) get_band_energy() (DOS method) (LDOS method) get_best_trial_results() (HyperOptNASWOT method) (HyperOptOAT method) get_beta() (in module mala.targets.calculation_helpers) get_categorical() (HyperparameterOAT method) (HyperparameterOptuna method) get_comm() (in module mala.common.parallelizer) get_density() (Density method) (LDOS method) get_density_of_states() (DOS method) (LDOS method) get_energy_contributions() (Density method) get_energy_grid() (DOS method) (LDOS method) (Target method) get_energy_targets_and_predictions() (Tester method) get_entropy_contribution() (DOS method) (LDOS method) get_equilibrated_configuration() (OFDFTInitializer method) get_f0_value() (in module mala.targets.calculation_helpers) get_f1_value() (in module mala.targets.calculation_helpers) get_f2_value() (in module mala.targets.calculation_helpers) get_feature_size() (AtomicForce method) get_first_snapshot() (TrajectoryAnalyzer method) get_float() (HyperparameterOptuna method) get_int() (HyperparameterOptuna method)

get_local_rank() (in module mala.common.parallelizer) get_new_data() (LazyLoadDataset method) get_number_of_electrons() (Density method) (DOS method) (LDOS method) get_optimal_parameters() (HyperOptOAT method) get_optimal_sigma() (AtomicDensity static method) get_orthogonal_array() (HyperOptOAT method) get_parameter() (HyperparameterOAT method) (HyperparameterOptuna method) get_radial_distribution_function() (Target method) get_rank() (in module mala.common.parallelizer) get_real_space_grid() (Target method) get_s0_value() (in module mala.targets.calculation_helpers) get_s1_value() (in module mala.targets.calculation_helpers) get_scaled_positions_for_qe() (Density static method) get_self_consistent_fermi_energy() (DOS method) (LDOS method) get_size() (in module mala.common.parallelizer) get_snapshot_calculation_output() (DataHandler method) get_snapshot_correlation_cutoff() (TrajectoryAnalyzer method) get_static_structure_factor() (Target method) get_target() (Density method) (DOS method) (LDOS method) (Target method) get_test_input_gradient() (DataHandler method) get_three_particle_correlation_function() (Target method) get_total_energy() (LDOS method) get_trials_from_study() (HyperOptOptuna method) get_uncorrelated_snapshots() (TrajectoryAnalyzer method) GRU (class in mala.network.network)

H

hlist (ParametersHyperparameterOptimization attribute) HyperOpt (class in mala.network.hyper_opt) HyperOptNASWOT (class in mala.network.hyper_opt_naswot) HyperOptOAT (class in mala.network.hyper_opt_oat) HyperOptOptuna (class in mala.network.hyper_opt_optuna)

Hyperparameter (class in mala.network.hyperparameter) HyperparameterACSD (class in mala.network.hyperparameter_acsd) HyperparameterNASWOT (class in mala.network.hyperparameter_naswot) HyperparameterOAT (class in mala.network.hyperparameter_oat) HyperparameterOptuna (class in mala.network.hyperparameter_optuna) hyperparameters (Parameters attribute)

I

implemented_properties (MALA attribute) incremental_fit() (DataScaler method) inference_data_grid (ParametersRunning attribute) init_hidden() (GRU method) (LSTM method) init_weights() (TransformerNet method) input_dimension (DataHandlerBase property)

input_rescaling_type (ParametersData attribute) integrate_values_on_spacing() (in module mala.targets.calculation_helpers) invalidate_target() (Density method) (DOS method) (LDOS method) (Target method) inverse_transform() (DataScaler method)

J

JSONSerializable (class in mala.common.json_serializable)

L

lammps_compute_file (ParametersDescriptors attribute) layer_activations (ParametersNetwork attribute) layer_sizes (ParametersNetwork attribute) LazyLoadDataset (class in mala.datahandling.lazy_load_dataset) LazyLoadDatasetSingle (class in mala.datahandling.lazy_load_dataset_single) LDOS (class in mala.targets.ldos) ldos_gridoffset_ev (ParametersTargets attribute) ldos_gridsize (ParametersTargets attribute) ldos_gridspacing_ev (ParametersTargets attribute) LDOSAligner (class in mala.datahandling.ldos_aligner) learning_rate (ParametersRunning attribute) learning_rate_decay (ParametersRunning attribute) learning_rate_patience (ParametersRunning attribute) learning_rate_scheduler (ParametersRunning attribute) load_from_file() (DataScaler class method) (HyperOptOAT class method) (HyperOptOptuna class method) (Network class method) (Parameters class method)

load_from_json() (Parameters class method) load_from_pickle() (Parameters class method) load_model() (MALA class method) load_run() (MALA class method) (Runner class method) (Trainer class method) load_snapshot_to_shm() (MultiLazyLoadDataLoader static method) local_density_of_states (LDOS property) local_psp_name (ParametersDataGeneration attribute) local_psp_path (ParametersDataGeneration attribute) logging_dir (ParametersRunning attribute) logging_dir_append_date (ParametersRunning attribute) loss_function_type (ParametersNetwork attribute) LSTM (class in mala.network.network)

M

mala module MALA (class in mala.interfaces.ase_calculator) mala.common module mala.common.check_modules module mala.common.json_serializable module mala.common.parallelizer module mala.common.parameters module mala.common.physical_data module mala.datageneration module mala.datageneration.ofdft_initializer module mala.datageneration.trajectory_analyzer module mala.datahandling module mala.datahandling.data_converter module mala.datahandling.data_handler module mala.datahandling.data_handler_base module mala.datahandling.data_repo module mala.datahandling.data_scaler module mala.datahandling.data_shuffler module mala.datahandling.fast_tensor_dataset module mala.datahandling.lazy_load_dataset module mala.datahandling.lazy_load_dataset_single module mala.datahandling.ldos_aligner module mala.datahandling.multi_lazy_load_data_loader module mala.datahandling.snapshot module mala.descriptors module mala.descriptors.atomic_density module mala.descriptors.bispectrum module mala.descriptors.descriptor module mala.descriptors.lammps_utils module mala.descriptors.minterpy_descriptors module mala.interfaces module mala.interfaces.ase_calculator module mala.network module mala.network.acsd_analyzer module mala.network.hyper_opt module mala.network.hyper_opt_naswot module mala.network.hyper_opt_oat module mala.network.hyper_opt_optuna module mala.network.hyperparameter module mala.network.hyperparameter_acsd module mala.network.hyperparameter_naswot module mala.network.hyperparameter_oat module mala.network.hyperparameter_optuna module mala.network.multi_training_pruner module mala.network.naswot_pruner module mala.network.network module mala.network.objective_base module mala.network.objective_naswot module mala.network.predictor module

mala.network.runner module mala.network.tester module mala.network.trainer module mala.targets module mala.targets.atomic_force module mala.targets.calculation_helpers module mala.targets.cube_parser module mala.targets.density module mala.targets.dos module mala.targets.ldos module mala.targets.target module mala.targets.xsf_parser module mala.version module manual_seed (Parameters attribute) max_number_epochs (ParametersRunning attribute) mini_batch_size (ParametersRunning attribute) MinterpyDescriptors (class in mala.descriptors.minterpy_descriptors) mix_datasets() (DataHandler method) (LazyLoadDataset method) (LazyLoadDatasetSingle method) module mala mala.common mala.common.check_modules mala.common.json_serializable mala.common.parallelizer mala.common.parameters mala.common.physical_data mala.datageneration mala.datageneration.ofdft_initializer mala.datageneration.trajectory_analyzer mala.datahandling mala.datahandling.data_converter mala.datahandling.data_handler mala.datahandling.data_handler_base mala.datahandling.data_repo mala.datahandling.data_scaler mala.datahandling.data_shuffler mala.datahandling.fast_tensor_dataset mala.datahandling.lazy_load_dataset mala.datahandling.lazy_load_dataset_single mala.datahandling.ldos_aligner mala.datahandling.multi_lazy_load_data_loader mala.datahandling.snapshot mala.descriptors mala.descriptors.atomic_density mala.descriptors.bispectrum mala.descriptors.descriptor mala.descriptors.lammps_utils mala.descriptors.minterpy_descriptors mala.interfaces mala.interfaces.ase_calculator mala.network mala.network.acsd_analyzer mala.network.hyper_opt mala.network.hyper_opt_naswot mala.network.hyper_opt_oat mala.network.hyper_opt_optuna mala.network.hyperparameter mala.network.hyperparameter_acsd mala.network.hyperparameter_naswot mala.network.hyperparameter_oat mala.network.hyperparameter_optuna mala.network.multi_training_pruner mala.network.naswot_pruner mala.network.network mala.network.objective_base mala.network.objective_naswot mala.network.predictor mala.network.runner mala.network.tester mala.network.trainer mala.targets mala.targets.atomic_force mala.targets.calculation_helpers mala.targets.cube_parser mala.targets.density mala.targets.dos mala.targets.ldos mala.targets.target mala.targets.xsf_parser mala.version MultiLazyLoadDataLoader (class in mala.datahandling.multi_lazy_load_data_loader) MultiTrainingPruner (class in mala.network.multi_training_pruner)

N

n_trials (ParametersHyperparameterOptimization attribute) NASWOTPruner (class in mala.network.naswot_pruner) Network (class in mala.network.network) network (Parameters attribute) nn_type (ParametersNetwork attribute) no_hidden_state (ParametersNetwork attribute) num_choices (HyperparameterOAT property)

num_heads (ParametersNetwork attribute) num_hidden_layers (ParametersNetwork attribute) num_workers (ParametersRunning attribute) number_of_electrons (Density property) (DOS property) (LDOS property) number_of_runs() (HyperOptOAT method) number_training_per_trial (ParametersHyperparameterOptimization property)

O

ObjectiveBase (class in mala.network.objective_base) ObjectiveNASWOT (class in mala.network.objective_naswot) ofdft_friction (ParametersDataGeneration attribute) ofdft_kedf (ParametersDataGeneration attribute) ofdft_number_of_timesteps (ParametersDataGeneration attribute) ofdft_temperature (ParametersDataGeneration attribute) ofdft_timestep (ParametersDataGeneration attribute)

OFDFTInitializer (class in mala.datageneration.ofdft_initializer) openpmd_configuration (Parameters property) openpmd_granularity (Parameters property) optimizer (ParametersRunning attribute) optuna_singlenode_setup() (Parameters method) output_dimension (DataHandlerBase property) output_rescaling_type (ParametersData attribute)

P

parallel_warn() (in module mala.common.parallelizer) Parameters (class in mala.common.parameters) ParametersBase (class in mala.common.parameters) ParametersData (class in mala.common.parameters) ParametersDataGeneration (class in mala.common.parameters) ParametersDescriptors (class in mala.common.parameters) ParametersHyperparameterOptimization (class in mala.common.parameters) ParametersNetwork (class in mala.common.parameters) ParametersRunning (class in mala.common.parameters) ParametersTargets (class in mala.common.parameters) parse_trial() (ObjectiveBase method) parse_trial_oat() (ObjectiveBase method) parse_trial_optuna() (ObjectiveBase method) perform_study() (ACSDAnalyzer method) (HyperOpt method) (HyperOptNASWOT method) (HyperOptOAT method) (HyperOptOptuna method)

PhysicalData (class in mala.common.physical_data) PhysicalData.SkipArrayWriting (class in mala.common.physical_data) PositionalEncoding (class in mala.network.network) predict_for_atoms() (Predictor method) predict_from_qeout() (Predictor method) predict_targets() (Tester method) Predictor (class in mala.network.predictor) prepare_data() (DataHandler method) prepare_for_testing() (DataHandler method) printout() (in module mala.common.parallelizer) profiler_range (ParametersRunning attribute) prune() (MultiTrainingPruner method) (NASWOTPruner method) pseudopotential_path (ParametersTargets attribute)

Q

qe_input_data (Target property)

R

radial_distribution_function_from_atoms() (Target static method) raw_numpy_to_converted_scaled_tensor() (DataHandler method) rdb_storage_heartbeat (ParametersHyperparameterOptimization property) rdf_parameters (ParametersTargets attribute) read_additional_calculation_data() (Target method) read_cube() (in module mala.targets.cube_parser) read_dimensions_from_numpy_file() (PhysicalData method) read_dimensions_from_openpmd_file() (PhysicalData method) read_from_array() (Density method) (DOS method) (LDOS method) read_from_cube() (Density method) (LDOS method) read_from_numpy_file() (DOS method) (PhysicalData method) read_from_openpmd_file() (PhysicalData method) read_from_qe_dos_txt() (DOS method)

read_from_qe_out() (DOS method) read_from_xsf() (Density method) (LDOS method) read_imcube() (in module mala.targets.cube_parser) read_xsf() (in module mala.targets.xsf_parser) readline() (CubeFile method) requeue_zombie_trials() (HyperOptOptuna static method) resize_snapshots_for_debugging() (DataHandler method) restrict_data() (Target method) restrict_targets (ParametersTargets property) resume_checkpoint() (HyperOptOAT class method) (HyperOptOptuna class method) return_outputs_directly (LazyLoadDataset property) run_exists() (Runner class method) (Trainer class method) Runner (class in mala.network.runner) running (Parameters attribute)

S

save() (DataScaler method) (Parameters method) save_as_json() (Parameters method) save_as_pickle() (Parameters method) save_calculator() (MALA method) save_network() (Network method) save_run() (Runner method) set_cmdlinevars() (in module mala.descriptors.lammps_utils) set_current_verbosity() (in module mala.common.parallelizer) set_ddp_status() (in module mala.common.parallelizer) set_lammps_instance() (in module mala.common.parallelizer) set_mpi_status() (in module mala.common.parallelizer) set_optimal_parameters() (ACSDAnalyzer method) (HyperOpt method) (HyperOptNASWOT method) (HyperOptOAT method) (HyperOptOptuna method) set_parameters() (HyperOpt method) setup_lammps_tmp_files() (Descriptor method) show() (Parameters method) (ParametersBase method) (ParametersHyperparameterOptimization method)

show_order_of_importance() (HyperOptOAT method) shuffle() (FastTensorDataset method) shuffle_snapshots() (DataShuffler method) shuffling_seed (ParametersData attribute) si_dimension (Density property) (Descriptor property) (DOS property) (LDOS property) (PhysicalData property) (Target property) si_unit_conversion (Density property) (Descriptor property) (DOS property) (LDOS property) (PhysicalData property) (Target property) Snapshot (class in mala.datahandling.snapshot) snapshot_correlation_cutoff (TrajectoryAnalyzer property) snapshot_directories_list (ParametersData attribute) ssf_parameters (ParametersTargets attribute) start_incremental_fitting() (DataScaler method) static_structure_factor_from_atoms() (Target static method)

T

Target (class in mala.targets.target) target_calculator (DataConverter attribute) target_type (ParametersTargets attribute) targets (Parameters attribute) te_mutex (Density attribute) test_all_snapshots() (Tester method) test_snapshot() (Tester method) Tester (class in mala.network.tester) three_particle_correlation_function_from_atoms() (Target static method) to_json() (JSONSerializable method) (ParametersBase method) total_energy (LDOS property) total_energy_contributions (Density property)

tpcf_parameters (ParametersTargets attribute) train_network() (Trainer method) Trainer (class in mala.network.trainer) training_log_interval (ParametersRunning attribute) trajectory (TrajectoryAnalyzer property) trajectory_analysis_below_average_counter (ParametersDataGeneration attribute) trajectory_analysis_correlation_metric_cutoff (ParametersDataGeneration attribute) trajectory_analysis_denoising_width (ParametersDataGeneration attribute) trajectory_analysis_estimated_equilibrium (ParametersDataGeneration attribute) trajectory_analysis_temperature_tolerance_percent (ParametersDataGeneration attribute) TrajectoryAnalyzer (class in mala.datageneration.trajectory_analyzer) transform() (DataScaler method) TransformerNet (class in mala.network.network) trial_ensemble_evaluation (ParametersHyperparameterOptimization property)

U

uncache_properties() (Density method) (DOS method) (LDOS method) (TrajectoryAnalyzer method) use_atomic_density_formula (Parameters property) use_ddp (Parameters property) use_fast_tensor_data_set (ParametersData attribute) use_gpu (Parameters property)

use_graphs (ParametersRunning property) use_lammps (Parameters property) use_lazy_loading (ParametersData attribute) use_lazy_loading_prefetch (ParametersData attribute) use_mixed_precision (ParametersRunning attribute) use_mpi (Parameters property) use_shuffling_for_samplers (ParametersRunning attribute) use_y_splitting (ParametersDescriptors property) use_z_splitting (ParametersDescriptors property)

V

verbosity (Parameters property)

W

write_additional_calculation_data() (Target method) write_cube() (in module mala.targets.cube_parser) write_imcube() (in module mala.targets.cube_parser) write_tem_input_file() (Target static method) write_to_cube() (Density method)

write_to_numpy_file() (PhysicalData method) (Target method) write_to_openpmd_file() (Density method) (PhysicalData method) (Target method) write_to_openpmd_iteration() (PhysicalData method)