Framework for electronic structure learning.

Can be used to preprocess DFT data (positions / LDOS), train networks, predict LDOS and postprocess LDOS into energies (and forces, soon).

mala

• common
  • check_modules
    • check_modules()
  • json_serializable
    • JSONSerializable
      • JSONSerializable.from_json()
      • JSONSerializable.to_json()
  • parallelizer
    • barrier()
    • finalize()
    • get_comm()
    • get_local_rank()
    • get_rank()
    • get_size()
    • parallel_warn()
    • printout()
    • set_current_verbosity()
    • set_ddp_status()
    • set_lammps_instance()
    • set_mpi_status()
  • parameters
    • Parameters
      • Parameters.comment
      • Parameters.network
      • Parameters.descriptors
      • Parameters.targets
      • Parameters.data
      • Parameters.running
      • Parameters.hyperparameters
      • Parameters.manual_seed
      • Parameters.load_from_file()
      • Parameters.load_from_json()
      • Parameters.load_from_pickle()
      • Parameters.optuna_singlenode_setup()
      • Parameters.save()
      • Parameters.save_as_json()
      • Parameters.save_as_pickle()
      • Parameters.show()
      • Parameters.device
      • Parameters.openpmd_configuration
      • Parameters.openpmd_granularity
      • Parameters.use_atomic_density_formula
      • Parameters.use_ddp
      • Parameters.use_gpu
      • Parameters.use_lammps
      • Parameters.use_mpi
      • Parameters.verbosity
    • ParametersBase
      • ParametersBase.from_json()
      • ParametersBase.show()
      • ParametersBase.to_json()
    • ParametersData
      • ParametersData.snapshot_directories_list
      • ParametersData.data_splitting_type
      • ParametersData.input_rescaling_type
      • ParametersData.output_rescaling_type
      • ParametersData.use_lazy_loading
      • ParametersData.use_lazy_loading_prefetch
      • ParametersData.use_fast_tensor_data_set
      • ParametersData.shuffling_seed
    • ParametersDataGeneration
      • ParametersDataGeneration.trajectory_analysis_denoising_width
      • ParametersDataGeneration.trajectory_analysis_below_average_counter
      • ParametersDataGeneration.trajectory_analysis_estimated_equilibrium
      • ParametersDataGeneration.trajectory_analysis_correlation_metric_cutoff
      • ParametersDataGeneration.trajectory_analysis_temperature_tolerance_percent
      • ParametersDataGeneration.local_psp_path
      • ParametersDataGeneration.local_psp_name
      • ParametersDataGeneration.ofdft_timestep
      • ParametersDataGeneration.ofdft_number_of_timesteps
      • ParametersDataGeneration.ofdft_temperature
      • ParametersDataGeneration.ofdft_kedf
      • ParametersDataGeneration.ofdft_friction
    • ParametersDescriptors
      • ParametersDescriptors.descriptor_type
      • ParametersDescriptors.bispectrum_twojmax
      • ParametersDescriptors.lammps_compute_file
      • ParametersDescriptors.descriptors_contain_xyz
      • ParametersDescriptors.atomic_density_sigma
      • ParametersDescriptors.bispectrum_cutoff
      • ParametersDescriptors.bispectrum_switchflag
      • ParametersDescriptors.use_y_splitting
      • ParametersDescriptors.use_z_splitting
    • ParametersHyperparameterOptimization
      • ParametersHyperparameterOptimization.direction
      • ParametersHyperparameterOptimization.n_trials
      • ParametersHyperparameterOptimization.hlist
      • ParametersHyperparameterOptimization.show()
      • ParametersHyperparameterOptimization.number_training_per_trial
      • ParametersHyperparameterOptimization.rdb_storage_heartbeat
      • ParametersHyperparameterOptimization.trial_ensemble_evaluation
    • ParametersNetwork
      • ParametersNetwork.nn_type
      • ParametersNetwork.layer_sizes
      • ParametersNetwork.layer_activations
      • ParametersNetwork.loss_function_type
      • ParametersNetwork.no_hidden_state
      • ParametersNetwork.bidirection
      • ParametersNetwork.num_hidden_layers
      • ParametersNetwork.num_heads
    • ParametersRunning
      • ParametersRunning.optimizer
      • ParametersRunning.learning_rate
      • ParametersRunning.max_number_epochs
      • ParametersRunning.mini_batch_size
      • ParametersRunning.early_stopping_epochs
      • ParametersRunning.early_stopping_threshold
      • ParametersRunning.learning_rate_scheduler
      • ParametersRunning.learning_rate_decay
      • ParametersRunning.learning_rate_patience
      • ParametersRunning.num_workers
      • ParametersRunning.use_shuffling_for_samplers
      • ParametersRunning.checkpoints_each_epoch
      • ParametersRunning.checkpoint_name
      • ParametersRunning.logging_dir
      • ParametersRunning.logging_dir_append_date
      • ParametersRunning.inference_data_grid
      • ParametersRunning.use_mixed_precision
      • ParametersRunning.training_log_interval
      • ParametersRunning.profiler_range
      • ParametersRunning.after_training_metric
      • ParametersRunning.during_training_metric
      • ParametersRunning.use_graphs
    • ParametersTargets
      • ParametersTargets.target_type
      • ParametersTargets.ldos_gridsize
      • ParametersTargets.ldos_gridspacing_ev
      • ParametersTargets.ldos_gridoffset_ev
      • ParametersTargets.pseudopotential_path
      • ParametersTargets.rdf_parameters
      • ParametersTargets.tpcf_parameters
      • ParametersTargets.ssf_parameters
      • ParametersTargets.assume_two_dimensional
      • ParametersTargets.restrict_targets
  • physical_data
    • PhysicalData
      • PhysicalData.SkipArrayWriting
      • PhysicalData.read_dimensions_from_numpy_file()
      • PhysicalData.read_dimensions_from_openpmd_file()
      • PhysicalData.read_from_numpy_file()
      • PhysicalData.read_from_openpmd_file()
      • PhysicalData.write_to_numpy_file()
      • PhysicalData.write_to_openpmd_file()
      • PhysicalData.write_to_openpmd_iteration()
      • PhysicalData.data_name
      • PhysicalData.feature_size
      • PhysicalData.si_dimension
      • PhysicalData.si_unit_conversion
• datageneration
  • ofdft_initializer
    • OFDFTInitializer
      • OFDFTInitializer.get_equilibrated_configuration()
  • trajectory_analyzer
    • TrajectoryAnalyzer
      • TrajectoryAnalyzer.get_first_snapshot()
      • TrajectoryAnalyzer.get_snapshot_correlation_cutoff()
      • TrajectoryAnalyzer.get_uncorrelated_snapshots()
      • TrajectoryAnalyzer.uncache_properties()
      • TrajectoryAnalyzer.first_snapshot
      • TrajectoryAnalyzer.snapshot_correlation_cutoff
      • TrajectoryAnalyzer.trajectory
• datahandling
  • data_converter
    • DataConverter
      • DataConverter.descriptor_calculator
      • DataConverter.target_calculator
      • DataConverter.add_snapshot()
      • DataConverter.convert_snapshots()
  • data_handler
    • DataHandler
      • DataHandler.clear_data()
      • DataHandler.get_snapshot_calculation_output()
      • DataHandler.get_test_input_gradient()
      • DataHandler.mix_datasets()
      • DataHandler.prepare_data()
      • DataHandler.prepare_for_testing()
      • DataHandler.raw_numpy_to_converted_scaled_tensor()
      • DataHandler.resize_snapshots_for_debugging()
  • data_handler_base
    • DataHandlerBase
      • DataHandlerBase.add_snapshot()
      • DataHandlerBase.clear_data()
      • DataHandlerBase.input_dimension
      • DataHandlerBase.output_dimension
  • data_repo
  • data_scaler
    • DataScaler
      • DataScaler.finish_incremental_fitting()
      • DataScaler.fit()
      • DataScaler.incremental_fit()
      • DataScaler.inverse_transform()
      • DataScaler.load_from_file()
      • DataScaler.save()
      • DataScaler.start_incremental_fitting()
      • DataScaler.transform()
  • data_shuffler
    • DataShuffler
      • DataShuffler.add_snapshot()
      • DataShuffler.shuffle_snapshots()
  • fast_tensor_dataset
    • FastTensorDataset
      • FastTensorDataset.shuffle()
  • lazy_load_dataset
    • LazyLoadDataset
      • LazyLoadDataset.add_snapshot_to_dataset()
      • LazyLoadDataset.get_new_data()
      • LazyLoadDataset.mix_datasets()
      • LazyLoadDataset.return_outputs_directly
  • lazy_load_dataset_single
    • LazyLoadDatasetSingle
      • LazyLoadDatasetSingle.allocate_shared_mem()
      • LazyLoadDatasetSingle.deallocate_shared_mem()
      • LazyLoadDatasetSingle.delete_data()
      • LazyLoadDatasetSingle.mix_datasets()
  • ldos_aligner
    • LDOSAligner
      • LDOSAligner.add_snapshot()
      • LDOSAligner.align_ldos_to_ref()
      • LDOSAligner.calc_optimal_ldos_shift()
  • multi_lazy_load_data_loader
    • MultiLazyLoadDataLoader
      • MultiLazyLoadDataLoader.cleanup()
      • MultiLazyLoadDataLoader.load_snapshot_to_shm()
  • snapshot
    • Snapshot
      • Snapshot.from_json()
• descriptors
  • atomic_density
    • AtomicDensity
      • AtomicDensity.backconvert_units()
      • AtomicDensity.convert_units()
      • AtomicDensity.get_optimal_sigma()
      • AtomicDensity.data_name
      • AtomicDensity.feature_size
  • bispectrum
    • Bispectrum
      • Bispectrum.backconvert_units()
      • Bispectrum.convert_units()
      • Bispectrum.data_name
      • Bispectrum.feature_size
  • descriptor
    • Descriptor
      • Descriptor.backconvert_units()
      • Descriptor.calculate_from_atoms()
      • Descriptor.calculate_from_qe_out()
      • Descriptor.convert_local_to_3d()
      • Descriptor.convert_units()
      • Descriptor.enforce_pbc()
      • Descriptor.gather_descriptors()
      • Descriptor.setup_lammps_tmp_files()
      • Descriptor.descriptors_contain_xyz
      • Descriptor.si_dimension
      • Descriptor.si_unit_conversion
  • lammps_utils
    • extract_compute_np()
    • set_cmdlinevars()
  • minterpy_descriptors
    • MinterpyDescriptors
      • MinterpyDescriptors.backconvert_units()
      • MinterpyDescriptors.convert_units()
      • MinterpyDescriptors.data_name
      • MinterpyDescriptors.feature_size
• interfaces
  • ase_calculator
    • MALA
      • MALA.calculate()
      • MALA.calculate_properties()
      • MALA.load_model()
      • MALA.load_run()
      • MALA.save_calculator()
      • MALA.implemented_properties
• network
  • acsd_analyzer
    • ACSDAnalyzer
      • ACSDAnalyzer.add_hyperparameter()
      • ACSDAnalyzer.add_snapshot()
      • ACSDAnalyzer.perform_study()
      • ACSDAnalyzer.set_optimal_parameters()
  • hyper_opt
    • HyperOpt
      • HyperOpt.add_hyperparameter()
      • HyperOpt.checkpoint_exists()
      • HyperOpt.clear_hyperparameters()
      • HyperOpt.perform_study()
      • HyperOpt.set_optimal_parameters()
      • HyperOpt.set_parameters()
  • hyper_opt_naswot
    • HyperOptNASWOT
      • HyperOptNASWOT.get_best_trial_results()
      • HyperOptNASWOT.perform_study()
      • HyperOptNASWOT.set_optimal_parameters()
  • hyper_opt_oat
    • HyperOptOAT
      • HyperOptOAT.add_hyperparameter()
      • HyperOptOAT.get_best_trial_results()
      • HyperOptOAT.get_optimal_parameters()
      • HyperOptOAT.get_orthogonal_array()
      • HyperOptOAT.load_from_file()
      • HyperOptOAT.number_of_runs()
      • HyperOptOAT.perform_study()
      • HyperOptOAT.resume_checkpoint()
      • HyperOptOAT.set_optimal_parameters()
      • HyperOptOAT.show_order_of_importance()
  • hyper_opt_optuna
    • HyperOptOptuna
      • HyperOptOptuna.get_trials_from_study()
      • HyperOptOptuna.load_from_file()
      • HyperOptOptuna.perform_study()
      • HyperOptOptuna.requeue_zombie_trials()
      • HyperOptOptuna.resume_checkpoint()
      • HyperOptOptuna.set_optimal_parameters()
  • hyperparameter
    • Hyperparameter
  • hyperparameter_acsd
    • HyperparameterACSD
  • hyperparameter_naswot
    • HyperparameterNASWOT
  • hyperparameter_oat
    • HyperparameterOAT
      • HyperparameterOAT.get_categorical()
      • HyperparameterOAT.get_parameter()
      • HyperparameterOAT.num_choices
  • hyperparameter_optuna
    • HyperparameterOptuna
      • HyperparameterOptuna.get_categorical()
      • HyperparameterOptuna.get_float()
      • HyperparameterOptuna.get_int()
      • HyperparameterOptuna.get_parameter()
  • multi_training_pruner
    • MultiTrainingPruner
      • MultiTrainingPruner.prune()
  • naswot_pruner
    • NASWOTPruner
      • NASWOTPruner.prune()
  • network
    • FeedForwardNet
      • FeedForwardNet.forward()
    • GRU
      • GRU.forward()
      • GRU.init_hidden()
    • LSTM
      • LSTM.forward()
      • LSTM.init_hidden()
    • Network
      • Network.calculate_loss()
      • Network.do_prediction()
      • Network.forward()
      • Network.load_from_file()
      • Network.save_network()
    • PositionalEncoding
      • PositionalEncoding.forward()
    • TransformerNet
      • TransformerNet.forward()
      • TransformerNet.generate_square_subsequent_mask()
      • TransformerNet.init_weights()
  • objective_base
    • ObjectiveBase
      • ObjectiveBase.parse_trial()
      • ObjectiveBase.parse_trial_oat()
      • ObjectiveBase.parse_trial_optuna()
  • objective_naswot
    • ObjectiveNASWOT
  • predictor
    • Predictor
      • Predictor.predict_for_atoms()
      • Predictor.predict_from_qeout()
  • runner
    • Runner
      • Runner.load_run()
      • Runner.run_exists()
      • Runner.save_run()
  • tester
    • Tester
      • Tester.get_energy_targets_and_predictions()
      • Tester.predict_targets()
      • Tester.test_all_snapshots()
      • Tester.test_snapshot()
  • trainer
    • Trainer
      • Trainer.load_run()
      • Trainer.run_exists()
      • Trainer.train_network()
• targets
  • atomic_force
    • AtomicForce
      • AtomicForce.convert_units()
      • AtomicForce.get_feature_size()
  • calculation_helpers
    • analytical_integration()
    • entropy_multiplicator()
    • fermi_function()
    • gaussians()
    • get_beta()
    • get_f0_value()
    • get_f1_value()
    • get_f2_value()
    • get_s0_value()
    • get_s1_value()
    • integrate_values_on_spacing()
  • cube_parser
    • CubeFile
      • CubeFile.readline()
    • read_cube()
    • read_imcube()
    • write_cube()
    • write_imcube()
  • density
    • Density
      • Density.backconvert_units()
      • Density.convert_units()
      • Density.from_cube_file()
      • Density.from_ldos_calculator()
      • Density.from_numpy_array()
      • Density.from_numpy_file()
      • Density.from_openpmd_file()
      • Density.from_xsf_file()
      • Density.get_atomic_forces()
      • Density.get_density()
      • Density.get_energy_contributions()
      • Density.get_number_of_electrons()
      • Density.get_scaled_positions_for_qe()
      • Density.get_target()
      • Density.invalidate_target()
      • Density.read_from_array()
      • Density.read_from_cube()
      • Density.read_from_xsf()
      • Density.uncache_properties()
      • Density.write_to_cube()
      • Density.write_to_openpmd_file()
      • Density.data_name
      • Density.density
      • Density.feature_size
      • Density.number_of_electrons
      • Density.si_dimension
      • Density.si_unit_conversion
      • Density.te_mutex
      • Density.total_energy_contributions
  • dos
    • DOS
      • DOS.backconvert_units()
      • DOS.convert_units()
      • DOS.from_ldos_calculator()
      • DOS.from_numpy_array()
      • DOS.from_numpy_file()
      • DOS.from_qe_dos_txt()
      • DOS.from_qe_out()
      • DOS.get_band_energy()
      • DOS.get_density_of_states()
      • DOS.get_energy_grid()
      • DOS.get_entropy_contribution()
      • DOS.get_number_of_electrons()
      • DOS.get_self_consistent_fermi_energy()
      • DOS.get_target()
      • DOS.invalidate_target()
      • DOS.read_from_array()
      • DOS.read_from_numpy_file()
      • DOS.read_from_qe_dos_txt()
      • DOS.read_from_qe_out()
      • DOS.uncache_properties()
      • DOS.band_energy
      • DOS.data_name
      • DOS.density_of_states
      • DOS.energy_grid
      • DOS.entropy_contribution
      • DOS.feature_size
      • DOS.fermi_energy
      • DOS.number_of_electrons
      • DOS.si_dimension
      • DOS.si_unit_conversion
  • ldos
    • LDOS
      • LDOS.backconvert_units()
      • LDOS.convert_units()
      • LDOS.from_cube_file()
      • LDOS.from_numpy_array()
      • LDOS.from_numpy_file()
      • LDOS.from_openpmd_file()
      • LDOS.from_xsf_file()
      • LDOS.get_atomic_forces()
      • LDOS.get_band_energy()
      • LDOS.get_density()
      • LDOS.get_density_of_states()
      • LDOS.get_energy_grid()
      • LDOS.get_entropy_contribution()
      • LDOS.get_number_of_electrons()
      • LDOS.get_self_consistent_fermi_energy()
      • LDOS.get_target()
      • LDOS.get_total_energy()
      • LDOS.invalidate_target()
      • LDOS.read_from_array()
      • LDOS.read_from_cube()
      • LDOS.read_from_xsf()
      • LDOS.uncache_properties()
      • LDOS.band_energy
      • LDOS.data_name
      • LDOS.density
      • LDOS.density_of_states
      • LDOS.energy_grid
      • LDOS.entropy_contribution
      • LDOS.feature_size
      • LDOS.fermi_energy
      • LDOS.local_density_of_states
      • LDOS.number_of_electrons
      • LDOS.si_dimension
      • LDOS.si_unit_conversion
      • LDOS.total_energy
  • target
    • Target
      • Target.backconvert_units()
      • Target.convert_units()
      • Target.get_energy_grid()
      • Target.get_radial_distribution_function()
      • Target.get_real_space_grid()
      • Target.get_static_structure_factor()
      • Target.get_target()
      • Target.get_three_particle_correlation_function()
      • Target.invalidate_target()
      • Target.radial_distribution_function_from_atoms()
      • Target.read_additional_calculation_data()
      • Target.restrict_data()
      • Target.static_structure_factor_from_atoms()
      • Target.three_particle_correlation_function_from_atoms()
      • Target.write_additional_calculation_data()
      • Target.write_tem_input_file()
      • Target.write_to_numpy_file()
      • Target.write_to_openpmd_file()
      • Target.feature_size
      • Target.qe_input_data
      • Target.si_dimension
      • Target.si_unit_conversion
  • xsf_parser
    • read_xsf()

• version