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
- json_serializable
- parallelizer
- parameters
ParametersParameters.commentParameters.networkParameters.descriptorsParameters.targetsParameters.dataParameters.runningParameters.hyperparametersParameters.manual_seedParameters.datagenerationParameters.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.deviceParameters.openpmd_configurationParameters.openpmd_granularityParameters.use_atomic_density_formulaParameters.use_ddpParameters.use_gpuParameters.use_lammpsParameters.use_mpiParameters.verbosity
ParametersBaseParametersDataParametersDataGenerationParametersDataGeneration.trajectory_analysis_denoising_widthParametersDataGeneration.trajectory_analysis_below_average_counterParametersDataGeneration.trajectory_analysis_estimated_equilibriumParametersDataGeneration.trajectory_analysis_correlation_metric_cutoffParametersDataGeneration.trajectory_analysis_temperature_tolerance_percentParametersDataGeneration.local_psp_pathParametersDataGeneration.local_psp_nameParametersDataGeneration.ofdft_timestepParametersDataGeneration.ofdft_number_of_timestepsParametersDataGeneration.ofdft_temperatureParametersDataGeneration.ofdft_kedfParametersDataGeneration.ofdft_friction
ParametersDescriptorsParametersDescriptors.descriptor_typeParametersDescriptors.bispectrum_twojmaxParametersDescriptors.descriptors_contain_xyzParametersDescriptors.atomic_density_sigmaParametersDescriptors.atomic_density_cutoffParametersDescriptors.lammps_compute_fileParametersDescriptors.minterpy_cutoff_cube_sizeParametersDescriptors.minterpy_lp_normParametersDescriptors.minterpy_point_listParametersDescriptors.minterpy_polynomial_degreeParametersDescriptors.bispectrum_cutoffParametersDescriptors.bispectrum_switchflagParametersDescriptors.use_y_splittingParametersDescriptors.use_z_splitting
ParametersHyperparameterOptimizationParametersHyperparameterOptimization.directionParametersHyperparameterOptimization.n_trialsParametersHyperparameterOptimization.hlistParametersHyperparameterOptimization.show()ParametersHyperparameterOptimization.number_training_per_trialParametersHyperparameterOptimization.rdb_storage_heartbeatParametersHyperparameterOptimization.trial_ensemble_evaluation
ParametersNetworkParametersRunningParametersRunning.optimizerParametersRunning.learning_rateParametersRunning.max_number_epochsParametersRunning.mini_batch_sizeParametersRunning.early_stopping_epochsParametersRunning.early_stopping_thresholdParametersRunning.learning_rate_schedulerParametersRunning.learning_rate_decayParametersRunning.learning_rate_patienceParametersRunning.num_workersParametersRunning.use_shuffling_for_samplersParametersRunning.checkpoints_each_epochParametersRunning.checkpoint_nameParametersRunning.run_nameParametersRunning.logging_dirParametersRunning.logging_dir_append_dateParametersRunning.loggerParametersRunning.validation_metricsParametersRunning.validate_on_training_dataParametersRunning.validate_every_n_epochsParametersRunning.training_log_intervalParametersRunning.profiler_rangeParametersRunning.inference_data_gridParametersRunning.use_mixed_precisionParametersRunning.l2_regularizationParametersRunning.dropoutParametersRunning.after_training_metricParametersRunning.during_training_metricParametersRunning.use_graphs
ParametersTargetsParametersTargets.target_typeParametersTargets.ldos_gridsizeParametersTargets.ldos_gridspacing_evParametersTargets.ldos_gridoffset_evParametersTargets.pseudopotential_pathParametersTargets.rdf_parametersParametersTargets.tpcf_parametersParametersTargets.ssf_parametersParametersTargets.assume_two_dimensionalParametersTargets.restrict_targets
- physical_data
PhysicalDataPhysicalData.parametersPhysicalData.grid_dimensionsPhysicalData.SkipArrayWritingPhysicalData.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_namePhysicalData.feature_sizePhysicalData.si_dimensionPhysicalData.si_unit_conversion
- datageneration
- ofdft_initializer
- trajectory_analyzer
TrajectoryAnalyzerTrajectoryAnalyzer.parametersTrajectoryAnalyzer.average_distance_equilibratedTrajectoryAnalyzer.distance_metrics_denoisedTrajectoryAnalyzer.distances_realspaceTrajectoryAnalyzer.first_considered_snapshotTrajectoryAnalyzer.last_considered_snapshotTrajectoryAnalyzer.target_calculatorTrajectoryAnalyzer.get_first_snapshot()TrajectoryAnalyzer.get_snapshot_correlation_cutoff()TrajectoryAnalyzer.get_uncorrelated_snapshots()TrajectoryAnalyzer.uncache_properties()TrajectoryAnalyzer.first_snapshotTrajectoryAnalyzer.snapshot_correlation_cutoffTrajectoryAnalyzer.trajectory
- datahandling
- data_converter
- data_handler
DataHandlerDataHandler.input_data_scalerDataHandler.nr_test_dataDataHandler.nr_test_snapshotsDataHandler.nr_training_dataDataHandler.nr_training_snapshotsDataHandler.nr_validation_dataDataHandler.nr_validation_snapshotsDataHandler.output_data_scalerDataHandler.test_data_setsDataHandler.training_data_setsDataHandler.validation_data_setsDataHandler.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
- data_repo
- data_scaler
DataScalerDataScaler.cantransformDataScaler.feature_wiseDataScaler.maxsDataScaler.meansDataScaler.minsDataScaler.scale_minmaxDataScaler.scale_standardDataScaler.stdsDataScaler.total_data_countDataScaler.total_maxDataScaler.total_meanDataScaler.total_minDataScaler.total_stdDataScaler.typestringDataScaler.use_ddpDataScaler.fit()DataScaler.inverse_transform()DataScaler.load_from_file()DataScaler.partial_fit()DataScaler.reset()DataScaler.save()DataScaler.transform()
- data_shuffler
- fast_tensor_dataset
- lazy_load_dataset
- lazy_load_dataset_single
LazyLoadDatasetSingleLazyLoadDatasetSingle.allocatedLazyLoadDatasetSingle.currently_loaded_fileLazyLoadDatasetSingle.descriptor_calculatorLazyLoadDatasetSingle.input_dataLazyLoadDatasetSingle.input_dtypeLazyLoadDatasetSingle.input_shapeLazyLoadDatasetSingle.input_shm_nameLazyLoadDatasetSingle.loadedLazyLoadDatasetSingle.output_dataLazyLoadDatasetSingle.output_dtypeLazyLoadDatasetSingle.output_shapeLazyLoadDatasetSingle.output_shm_nameLazyLoadDatasetSingle.return_outputs_directlyLazyLoadDatasetSingle.snapshotLazyLoadDatasetSingle.target_calculatorLazyLoadDatasetSingle.allocate_shared_mem()LazyLoadDatasetSingle.deallocate_shared_mem()LazyLoadDatasetSingle.delete_data()LazyLoadDatasetSingle.mix_datasets()
- ldos_aligner
- multi_lazy_load_data_loader
- snapshot
SnapshotSnapshot.grid_dimensionsSnapshot.grid_sizeSnapshot.input_dimensionSnapshot.output_dimensionSnapshot.input_npy_fileSnapshot.input_npy_directorySnapshot.output_npy_fileSnapshot.output_npy_directorySnapshot.input_unitsSnapshot.output_unitsSnapshot.calculation_outputSnapshot.snapshot_functionSnapshot.snapshot_typeSnapshot.from_json()
- descriptors
- atomic_density
- bispectrum
- descriptor
DescriptorDescriptor.parametersDescriptor.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_xyzDescriptor.feature_sizeDescriptor.si_dimensionDescriptor.si_unit_conversion
- lammps_utils
- minterpy_descriptors
- interfaces
- network
- acsd_analyzer
- descriptor_scoring_optimizer
- hyper_opt
- hyper_opt_naswot
- hyper_opt_oat
- hyper_opt_optuna
- hyperparameter
- hyperparameter_descriptor_scoring
- hyperparameter_naswot
- hyperparameter_oat
- hyperparameter_optuna
- multi_training_pruner
- mutual_information_analyzer
- naswot_pruner
- network
- objective_base
- objective_naswot
- predictor
- runner
- tester
- trainer
- targets
- atomic_force
- calculation_helpers
- cube_parser
- density
DensityDensity.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_nameDensity.densityDensity.feature_sizeDensity.number_of_electronsDensity.si_dimensionDensity.si_unit_conversionDensity.te_mutexDensity.total_energy_contributions
- dos
DOSDOS.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_energyDOS.data_nameDOS.density_of_statesDOS.energy_gridDOS.entropy_contributionDOS.feature_sizeDOS.fermi_energyDOS.number_of_electronsDOS.si_dimensionDOS.si_unit_conversion
- ldos
LDOSLDOS.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_energyLDOS.data_nameLDOS.densityLDOS.density_of_statesLDOS.energy_gridLDOS.entropy_contributionLDOS.feature_sizeLDOS.fermi_energyLDOS.local_density_of_statesLDOS.number_of_electronsLDOS.si_dimensionLDOS.si_unit_conversionLDOS.total_energy
- target
TargetTarget.atomic_forces_dftTarget.atomsTarget.band_energy_dft_calculationTarget.electrons_per_atomTarget.entropy_contribution_dft_calculationTarget.fermi_energy_dftTarget.kpointsTarget.local_gridTarget.number_of_electrons_exactTarget.number_of_electrons_from_eigenvalsTarget.parametersTarget.qe_pseudopotentialsTarget.save_target_dataTarget.temperatureTarget.total_energy_contributions_dft_calculationTarget.total_energy_dft_calculationTarget.voxelTarget.y_planesTarget.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_sizeTarget.qe_input_dataTarget.si_dimensionTarget.si_unit_conversion
- xsf_parser