General functions for MALA, such as parameters.

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.datageneration
    • 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.descriptors_contain_xyz
    • ParametersDescriptors.atomic_density_sigma
    • ParametersDescriptors.atomic_density_cutoff
    • ParametersDescriptors.lammps_compute_file
    • ParametersDescriptors.minterpy_cutoff_cube_size
    • ParametersDescriptors.minterpy_lp_norm
    • ParametersDescriptors.minterpy_point_list
    • ParametersDescriptors.minterpy_polynomial_degree
    • 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
    • ParametersNetwork.dropout
  • 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.run_name
    • ParametersRunning.logging_dir
    • ParametersRunning.logging_dir_append_date
    • ParametersRunning.logger
    • ParametersRunning.validation_metrics
    • ParametersRunning.validate_on_training_data
    • ParametersRunning.validate_every_n_epochs
    • ParametersRunning.training_log_interval
    • ParametersRunning.profiler_range
    • ParametersRunning.inference_data_grid
    • ParametersRunning.use_mixed_precision
    • ParametersRunning.l2_regularization
    • ParametersRunning.dropout
    • 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.parameters
    • PhysicalData.grid_dimensions
    • PhysicalData.SkipArrayWriting
      • PhysicalData.SkipArrayWriting.dataset
      • PhysicalData.SkipArrayWriting.feature_size
    • 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