Index

_

__call__() (AddAtomCooIndices method) (AddBasisInfo method) (AddCoulombMatrix method) (AddLocalFrames method) (AddMol method) (AddNuclearAttractionVector method) (AddOverlapMatrix method) (BasicCallback method) (MinorSymLogLocator method) (OFCollater method) (SplitByAtom method) (ToGlobalNatRep method) (ToLocalFrames method) (ToNumpy method) (ToTorch method) __cat_dim__() (OFData method) __enter__() (HierarchicalPlotPDF method) __eq__() (BaseConfig method) (BasicCallback method) (BasisInfo method) (ModelConfig method) (OFDFTRunResult method) (OFState method) (OptimizerConfig method) __exit__() (HierarchicalPlotPDF method) __format__() (ConvergenceCriterion method) (Representation method) (StrEnumwithCheck method) __getitem__() (Energies method) (OFDataset method) __inc__() (OFData method) __init__() (AddBasisInfo method) (AddCoulombMatrix method) (AddLocalFrames method) (AddMol method) (AddNuclearAttractionVector method) (AddOverlapMatrix method) (AddRadiusEdgeIndex method) (AnyRunCallback method) (AtomHotEmbedding method) (AtomRef method) (BaseConfig method) (BasicCallback method) (BasisInfo method) (DataCube method) (DataGenDataset method) (DatasetStatistics method) (DatasetStatisticsFitter method) (DimensionWiseRescaling method) (Energies method) (EveryIncreasingInterval method) (EveryNSteps method) (FullLoss method) (FunctionalFactory method) (G3DLayer method) (G3DLayerTF method) (G3DStack method) (GaussianLayer method) (GBFModule method) (GitInfo method) (GradientDescent method) (Graphformer method) (HierarchicalPlotPDF method) (InitialGuessDeltaModule method) (LocalBasisModule method) (LocalFramesModule method) (LocalFramesTransformMatrixDense method) (LocalFramesTransformMatrixSparse method) (LogDistanceEmbeddings method) (LogMolecule method) (LogTargetPredScatters method) (MasterTransformation method) (MinorSymLogLocator method) (MinSCFIterationSampleWeigher method) (MiscXYZ method) (MLDFTLitModule method) (MLP method) (MLPStack method) (ModelConfig method) (NegativeIntegratedDensity method) (NodeEmbedding method) (OFCollater method) (OFDataModule method) (OFDataset method) (OFDFTRunResult method) (OFLoader method) (OFState method) (OnStepCallbackWithTiming method) (OptimizerConfig method) (PerBasisFuncShrinkGateModule method) (PerSampleAbsoluteErrorMetric method) (PrintOverrides method) (ProductSampleWeigher method) (QM9 method) (QMUGS method) (QMUGSBin method) (QMUGSLargeBins method) (RankedLogger method) (SADGuesser method) (SampleGenerator method) (ShrinkGateModule method) (SimpleQuadraticAtomRef method) (SingleLossFunction method) (SLSQP method) (SmallDataset method) (SubModelSummary method) (ToGlobalNatRep method) (ToLocalFrames method) (TorchOptimizer method) (ToTorch method) (ToyEnergy method) (ToyInitialGuessDelta method) (ToyNet method) (TrustRegionConstrained method) (TwoElectronDataset method) (VectorAdam method) (WeightedLoss method)

__len__() (OFDataset method) __new__() (ConvergenceCriterion method) (Representation method) (StrEnumwithCheck method) __repr__() (BaseConfig method) (BasicCallback method) (DatasetStatistics method) (G3DLayer method) (G3DLayerTF method) (ModelConfig method) (OFDFTRunResult method) (OFState method) (OptimizerConfig method) __setattr__() (OFData method) __setitem__() (Energies method) (OFData method) __setstate__() (G3DLayer method) (G3DLayerTF method) (NodeEmbedding method) __str__() (ConvergenceCriterion method) (DataCube method) (Energies method) (FunctionalFactory method) (OFState method) (Optimizer method) (Representation method) (StrEnumwithCheck method) (TorchOptimizer method) _add_all_energy_differences() (in module mldft.utils.plotting.density_optimization) _add_coefficient_differences_lines() (in module mldft.utils.plotting.density_optimization) _add_coefficient_differences_pixels() (in module mldft.utils.plotting.density_optimization) _add_density_and_gradient() (in module mldft.utils.plotting.density_optimization) _add_density_difference() (in module mldft.utils.plotting.density_optimization) _add_energy_boxplot() (in module mldft.utils.plotting.summary_density_optimization) _add_energy_error_over_n_atoms() (in module mldft.utils.plotting.summary_density_optimization) _add_energy_histogram() (in module mldft.utils.plotting.summary_density_optimization) _add_energy_mae() (in module mldft.utils.plotting.summary_density_optimization) _add_gradient_norm() (in module mldft.utils.plotting.density_optimization) _add_integrated_negative_density() (in module mldft.utils.plotting.density_optimization) _add_mean_density_differences_l2() (in module mldft.utils.plotting.summary_density_optimization) _add_mean_gradient_norm() (in module mldft.utils.plotting.summary_density_optimization) _add_mean_relative_density_differences_l1() (in module mldft.utils.plotting.summary_density_optimization) _add_stopping_index_histogram() (in module mldft.utils.plotting.summary_density_optimization) _append_flat_gaussian() (in module mldft.ofdft.basis_integrals) _assert_shapes() (in module mldft.utils.coeffs_to_grid) _check_ao_dimensions_wrt_derivatives() (in module mldft.ofdft.libxc_functionals) _check_data_format() (in module mldft.datagen.methods.density_fitting) _compare_initial_to_stopping_gradient_norms() (in module mldft.utils.plotting.summary_density_optimization) _compare_initial_to_stopping_l2_norms() (in module mldft.utils.plotting.summary_density_optimization) _config_to_log_dict() (in module mldft.api.cli_ofdft) _create_train_val_test_split_dict() (in module mldft.utils.create_dataset_splits) _eval_density() (in module mldft.utils.visualize_3d) _eval_orbital() (in module mldft.utils.visualize_3d) _fix_cube_data() (in module mldft.utils.visualize_3d) _format_energies() (in module mldft.ofdft.energies) _format_energy() (in module mldft.ofdft.energies) _generate_next_value_() (ConvergenceCriterion static method) (Representation static method) (StrEnumwithCheck static method) _get_energy_and_functional_derivatives() (in module mldft.ofdft.libxc_functionals) _get_hydra_overrides() (in module mldft.ml.callbacks.print_overrides_callback) _get_leaf_key() (in module mldft.utils.omegaconf_resolvers) _get_one_center_integral() (in module mldft.ofdft.basis_integrals) _irreps_list_to_array() (in module mldft.ml.data.components.basis_info) _iteration_count() (in module mldft.utils.create_dataset_splits) _locate_logging_mixins_generator() (in module mldft.utils.log_utils.logging_mixin) _multi_shape_coeff_mae_scatter() (in module mldft.utils.plotting.summary_density_optimization) _on_anyrun_end() (AnyRunCallback method) _on_anyrun_start() (AnyRunCallback method) (GitInfo method) _process_log_dict() (LoggingMixin method) _save_additional_data_callback() (in module mldft.utils.plotting.plot_density_slices) _save_checkpoint() (ModelCheckpointWithPermissions method) _save_scf_iteration_callback() (in module mldft.datagen.methods.ksdft_calculation) _single_shape_coeff_mae_scatter() (in module mldft.utils.plotting.summary_density_optimization) _train_val_test_split() (in module mldft.utils.create_dataset_splits) _xc_type_to_deriv() (in module mldft.ofdft.libxc_functionals)

A

activate_logging() (LoggingMixin method) activate_logging_mixins() (MLDFTLitModule method) add_as_string_option() (in module mldft.utils.rich_utils) add_atom_coo_indices() (in module mldft.ml.data.components.convert_transforms) add_bookmark_dict() (in module mldft.utils.pdf_utils) add_density_optimization_trajectories_to_sample() (in module mldft.ofdft.run_density_optimization) add_item() (OFData method) add_new_axis() (in module mldft.utils.coeffs_to_grid) add_sad_kwargs() (in module mldft.api.cli_ofdft) AddAtomCooIndices (class in mldft.ml.data.components.convert_transforms) AddBasisInfo (class in mldft.ml.data.components.convert_transforms) AddCoulombMatrix (class in mldft.ml.data.components.convert_transforms) AddFullEdgeIndex (class in mldft.ml.data.components.convert_transforms) AddLocalFrames (class in mldft.ml.data.components.basis_transforms) AddMetricAndLossCustomScalars (class in mldft.ml.callbacks.custom_scalars) AddMol (class in mldft.ml.data.components.convert_transforms) AddNuclearAttractionVector (class in mldft.ml.data.components.convert_transforms) AddOverlapMatrix (class in mldft.ml.data.components.convert_transforms)

AddRadiusEdgeIndex (class in mldft.ml.data.components.convert_transforms) aggregate() (LocalBasisModule method) aggregate_distances() (NodeEmbedding method) AnyRunCallback (class in mldft.utils.log_utils.hydra_callbacks) apply_to_attributes() (in module mldft.ml.data.components.convert_transforms) apply_to_dataset_statistics() (DimensionWiseRescaling class method) ApplyBasisTransformation (class in mldft.ml.data.components.basis_transforms) ask_download_dataset_statistics() (in module mldft.api.setup) ask_download_models() (in module mldft.api.setup) ask_path() (in module mldft.api.setup) atom_ind (OFData attribute) atom_ind_to_basis_function_ind (BasisInfo attribute) atom_ptr (OFData attribute) AtomHotEmbedding (class in mldft.ml.models.components.density_coeff_embedding) atomic_number_to_atom_index (BasisInfo attribute) atomic_numbers (BasisInfo attribute) (OFData attribute) AtomRef (class in mldft.ml.models.components.atom_ref)

B

BaseConfig (class in mldft.api.instantiate_from_args) BasicCallback (class in mldft.ofdft.callbacks) basis_dict (BasisInfo attribute) basis_dim_per_atom (BasisInfo attribute) basis_func_to_shell (BasisInfo attribute) basis_function_ind (OFData attribute)

basis_info (SampleGenerator attribute) basis_transform() (MasterTransformation method) BasisInfo (class in mldft.ml.data.components.basis_info) build_mol_with_even_tempered_basis() (in module mldft.utils.molecules) build_molecule_np() (in module mldft.utils.molecules) build_molecule_ofdata() (in module mldft.utils.molecules)

C

calculate_basis_size() (in module mldft.ofdft.run_density_optimization) calculate_labels() (in module mldft.datagen.methods.label_generation) call_now() (CallbackTiming method) (EveryIncreasingInterval method) (EveryNSteps method) CallbackTiming (class in mldft.ml.callbacks.timing) chain_schedulers() (in module mldft.utils.lr_scheduling) check_atom_types() (in module mldft.utils.molecules) check_chk_file() (DataGenDataset static method) check_config() (in module mldft.datagen.kohn_sham_dataset) check_consistency() (BasisInfo method) check_key() (StrEnumwithCheck class method) check_kxc_implementation() (in module mldft.ofdft.libxc_functionals) check_paths_and_save() (in module mldft.utils.create_dataset_splits) checkpoint_path_to_run_number() (in module mldft.utils.omegaconf_resolvers) chem_formula_from_atomic_numbers() (in module mldft.utils.molecules) cleanup_via_smiles() (in module mldft.utils.draw_molecule) cleanup_xyz() (in module mldft.utils.draw_molecule) coeff_ind_to_node_ind (OFData attribute) CoefficientLoss (class in mldft.ml.models.components.loss_function) coeffs (BasicCallback attribute) (OFData attribute) (OFState attribute) coeffs_to_grad_rho() (in module mldft.utils.coeffs_to_grid) coeffs_to_laplace_rho() (in module mldft.utils.coeffs_to_grid) coeffs_to_rho() (in module mldft.utils.coeffs_to_grid) coeffs_to_rho_and_derivatives() (in module mldft.utils.coeffs_to_grid) collate() (in module mldft.ml.data.components.of_batch) combine_mesh_dicts() (in module mldft.ml.callbacks.mesh_logging) comparison_scatter() (in module mldft.utils.plotting.scatter) comparison_table() (Energies method) compute() (PerSampleAbsoluteErrorMetric method) compute_attention() (G3DLayer method) (G3DLayerMul method), [1] (G3DLayerMulSilu method), [1] (G3DLayerSilu method), [1] (G3DLayerTF method) compute_density_density_basis() (in module mldft.utils.grids)

compute_density_optimization_metrics() (in module mldft.ofdft.density_optimization) compute_density_orbital_basis() (in module mldft.utils.grids) compute_kohn_sham_dataset() (in module mldft.datagen.kohn_sham_dataset) compute_l1_norm_orbital_vs_density_basis() (in module mldft.utils.grids) compute_max_block_size() (in module mldft.utils.grids) compute_per_electron() (PerSampleAbsoluteErrorMetric method) compute_per_molecule() (PerSampleAbsoluteErrorMetric method) compute_spherical_average() (in module mldft.utils.sad_guesser) concatenate() (in module mldft.utils.coeffs_to_grid) configure_dataset_indices() (in module mldft.ofdft.run_density_optimization) configure_max_memory_per_process() (in module mldft.utils.multiprocess) configure_optimizers() (MLDFTLitModule method) configure_processes_and_threads() (in module mldft.utils.multiprocess) configure_scf_iterations() (OFDataset method) console_filter() (in module mldft.api.cli_ofdft) construct() (FunctionalFactory method) construct_aux_mol() (in module mldft.utils.molecules) construct_block_diag_coo_indices_and_shape() (in module mldft.utils.sparse) construct_block_diag_coo_tensor() (in module mldft.utils.sparse) construct_block_diag_coo_tensor_indices_and_shape_from_sparse() (in module mldft.utils.sparse) construct_coeffs() (in module mldft.utils.molecules) construct_new() (OFData class method) contract_coulomb_tensor() (in module mldft.datagen.methods.density_fitting) ConvergenceCallback (class in mldft.ofdft.callbacks) ConvergenceCriterion (class in mldft.ofdft.callbacks) ConvergenceError convert_folder_sorted_parallel() (in module mldft.datagen.datasets.qm9) convert_string_format() (in module mldft.datagen.datasets.qm9) convert_to_numpy() (BasicCallback method) convert_xyz_files() (QM9 method) convert_zarr_file() (in module mldft.datagen.transform_dataset) create_and_return_dir() (in module mldft.utils.omegaconf_resolvers) create_split_file() (in module mldft.utils.create_dataset_splits) create_split_file_qmugs_bin() (in module mldft.utils.create_custom_splits) create_split_file_qmugs_bin0_qm9() (in module mldft.utils.create_custom_splits) create_split_file_qmugs_large_bins() (in module mldft.utils.create_custom_splits) create_subset() (in module mldft.utils.create_subset) cumulate_coeff_error() (in module mldft.utils.plotting.summary_density_optimization) custom_round() (in module mldft.utils.plotting.summary_density_optimization)

D

data_class (OFDataset attribute) DataCube (class in mldft.utils.cube_files) DataGenDataset (class in mldft.datagen.datasets.dataset) dataset_class (OFDataModule attribute) DatasetStatistics (class in mldft.ml.preprocess.dataset_statistics) DatasetStatisticsFitter (class in mldft.ml.preprocess.dataset_statistics) deactivate_logging() (LoggingMixin method) deactivate_logging_mixins() (MLDFTLitModule method) default_log_timing() (in module mldft.ml.callbacks.base) delete_dataset() (in module mldft.datagen.datasets.dataset) delete_item() (OFData method) density_differences_swarm_line_plot() (in module mldft.utils.plotting.summary_density_optimization) density_fitting_hartree() (in module mldft.datagen.methods.density_fitting) density_fitting_hartree_external() (in module mldft.datagen.methods.density_fitting) density_fitting_hartree_external_fixed_density() (in module mldft.datagen.methods.density_fitting) density_fitting_hartree_fixed_density_external() (in module mldft.datagen.methods.density_fitting) density_fitting_mofdft() (in module mldft.datagen.methods.density_fitting) density_fitting_mofdft_enforced_density() (in module mldft.datagen.methods.density_fitting) density_fitting_mofdft_fixed_density() (in module mldft.datagen.methods.density_fitting) density_fitting_mofdft_torch() (in module mldft.datagen.methods.density_fitting) density_fitting_mol() (in module mldft.datagen.methods.density_fitting) density_optimization() (in module mldft.ofdft.density_optimization)

density_optimization_summary_pdf_plot() (in module mldft.utils.plotting.summary_density_optimization) density_optimization_swarm_plot() (in module mldft.utils.plotting.summary_density_optimization) density_optimization_with_label() (in module mldft.ofdft.density_optimization) dict_to_pyscf_dict() (in module mldft.utils.molecules) dict_to_tree() (in module mldft.utils.log_utils.config_in_tensorboard) diis_weighted_average() (in module mldft.datagen.methods.label_generation) DimensionWiseRescaling (class in mldft.ml.models.components.dimension_wise_rescaling) dir_counter() (in module mldft.utils.omegaconf_resolvers) directory_to_pdf_with_outline() (in module mldft.utils.pdf_utils) download() (DataGenDataset method) (MiscXYZ method) (QM9 method) (QM9Test method) (QMUGS method) (SmallDataset method) download_dataset_statistics() (in module mldft.api.setup) download_file() (in module mldft.utils.download) download_model() (in module mldft.api.setup) draw_molecule() (in module mldft.utils.draw_molecule) dtype_map() (in module mldft.ml.data.components.convert_transforms) dual_basis_integrals (OFData attribute) dumb_guess() (in module mldft.ofdft.initial_guess) dummy_run() (in module mldft.utils.log_utils.hydra_callbacks)

E

einsum() (in module mldft.utils.einsum) electronic_energy (Energies property) Energies (class in mldft.ofdft.energies) energies_dict (Energies attribute) energy (BasicCallback attribute) (OFState attribute) energy_error_swarm_line_plot() (in module mldft.utils.plotting.summary_density_optimization) ENERGY_UPDATE_GLOBAL_MINIMUM (StoppingCriterion attribute) ENERGY_UPDATE_STOPS_DECREASING (StoppingCriterion attribute) EnergyGradientLoss (class in mldft.ml.models.components.loss_function) EnergyLoss (class in mldft.ml.models.components.loss_function) enforce_tags() (in module mldft.utils.rich_utils) eval_density_functionals() (in module mldft.datagen.methods.label_generation)

eval_libxc_functionals() (in module mldft.ofdft.libxc_functionals) eval_torch_functionals() (in module mldft.ofdft.torch_functionals) eval_torch_functionals_blocked() (in module mldft.ofdft.torch_functionals) eval_torch_functionals_blocked_fast() (in module mldft.ofdft.torch_functionals) evaluate_functional() (FunctionalFactory method) EveryIncreasingInterval (class in mldft.ml.callbacks.timing) EveryNSteps (class in mldft.ml.callbacks.timing) execute() (LogMatplotlibToTensorboard method) (LogMolecule method) (OnStepCallbackWithTiming method) extract_group() (in module mldft.api.cli_ofdft) extract_tar() (in module mldft.utils.download) extras() (in module mldft.utils.utils)

F

find_isosurface_value() (in module mldft.utils.visualize_3d) fit() (DatasetStatisticsFitter method) format_basis_func_xaxis() (in module mldft.utils.plotting.axes) format_table_rich() (in module mldft.utils.rich_utils) forward() (AddFullEdgeIndex method) (AddRadiusEdgeIndex method) (ApplyBasisTransformation method) (AtomHotEmbedding method) (AtomRef method) (DimensionWiseRescaling method) (G3DLayer method) (G3DLayerTF method) (G3DStack method) (GaussianLayer method) (GBFModule method) (Graphformer method) (InitialGuessDeltaModule method) (LocalBasisModule method) (LocalFramesModule method) (LocalFramesTransformMatrixDense method) (LocalFramesTransformMatrixSparse method) (MasterTransformation method) (MLDFTLitModule method) (MLP method) (MLPStack method) (NegativeIntegratedDensity method) (NodeEmbedding method) (PerBasisFuncShrinkGateModule method) (ProjectGradient method) (SADGuesser method) (ShrinkGateModule method) (SimpleQuadraticAtomRef method) (SingleLossFunction method) (ToyEnergy method) (ToyInitialGuessDelta method) (ToyNet method) (WeightedLoss method)

from_atomic_numbers_with_even_tempered_basis() (BasisInfo class method) from_basis_info() (AtomHotEmbedding class method) (NodeEmbedding class method) from_data_list() (OFBatch class method) from_dataset() (DatasetStatistics static method) from_dataset_info_yaml() (BasisInfo class method) from_dataset_statistics() (AtomRef class method) (DimensionWiseRescaling class method) (SADGuesser class method) from_directory() (OFDataset class method) from_file() (DataCube class method) (OFData class method) from_file_with_all_gradients() (OFData class method) from_fileobject() (DataCube class method) from_function() (DataCube class method) from_module() (FunctionalFactory class method) from_mol() (BasisInfo class method) from_npz() (BasicCallback class method) from_nwchem() (BasisInfo class method) from_run_path() (SampleGenerator class method) FullLoss (class in mldft.ml.models.components.loss_function) FunctionalFactory (class in mldft.ofdft.functional_factory)

G

G3DLayer (class in mldft.ml.models.components.g3d_layer) G3DLayerMul (class in mldft.ml.models.components.g3d_layer) (class in mldft.ml.models.components.g3d_layer_tf) G3DLayerMulSilu (class in mldft.ml.models.components.g3d_layer) (class in mldft.ml.models.components.g3d_layer_tf) G3DLayerSilu (class in mldft.ml.models.components.g3d_layer) (class in mldft.ml.models.components.g3d_layer_tf) G3DLayerTF (class in mldft.ml.models.components.g3d_layer_tf) G3DStack (class in mldft.ml.models.components.g3d_stack) GaussianLayer (class in mldft.ml.models.components.gbf_module) GBFModule (class in mldft.ml.models.components.gbf_module) geometry_to_string() (in module mldft.utils.molecules) get_all_atomic_numbers() (DataGenDataset method) (MiscXYZ method) (QM9 method) (QMUGS method) (SmallDataset method) get_all_chk_files_from_id() (DataGenDataset method) get_all_chk_files_from_ids() (DataGenDataset method) get_and_increment_counter() (in module mldft.utils.counter_file) get_basis_dipole() (in module mldft.ofdft.basis_integrals) get_bin_from_num_atoms() (in module mldft.datagen.datasets.qmugs) get_chk_file_from_id() (DataGenDataset method) get_convergence_result() (ConvergenceCallback method) get_coulomb_matrix() (in module mldft.ofdft.basis_integrals) get_coulomb_tensor() (in module mldft.ofdft.basis_integrals) get_data_dict() (in module mldft.datagen.methods.label_generation) get_dataset_from_absolute_path() (in module mldft.utils.environ) get_density_difference_l1_norm() (in module mldft.utils.plotting.summary_density_optimization) get_density_difference_l2_norm() (in module mldft.utils.plotting.summary_density_optimization) get_density_fitting_function() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_hartree() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_hartree_external() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_hartree_external_fixed_density() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_hartree_fixed_density_external() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_mofdft() (in module mldft.datagen.methods.density_fitting) get_density_fitting_map_mofdft_fixed_density() (in module mldft.datagen.methods.density_fitting) get_distance_embeddings() (Graphformer method) get_energies_and_gradients() (in module mldft.datagen.methods.label_generation) get_energies_label() (FunctionalFactory method) get_energy_error() (in module mldft.utils.plotting.summary_density_optimization) get_energy_errors_dict() (in module mldft.utils.plotting.summary_density_optimization) get_figure() (LogDistanceEmbeddings method) (LogGradientScatter method) (LogMatplotlibToTensorboard method) (LogTargetPredScatters method) get_functional_factory() (SampleGenerator method) get_gga_potential_matrix() (in module mldft.ofdft.basis_integrals) get_gradient_descent_optimizer() (in module mldft.api.instantiate_from_args) get_gradient_descent_torch_optimizer() (in module mldft.api.instantiate_from_args) get_grid_blocks() (in module mldft.utils.grids) get_id_and_sample_id_from_chk_file() (in module mldft.datagen.generate_labels_dataset) get_ids() (DataGenDataset method) (MiscXYZ method) (QM9 method) (QMUGS method) (SmallDataset method) get_ids_done_ks() (DataGenDataset method) get_ids_done_labelgen() (DataGenDataset method) get_ids_todo_ks() (DataGenDataset method) get_ids_todo_labelgen() (DataGenDataset method)

get_irreps_and_integrals() (BasisInfo class method) get_KSDFT_Hartree_potential() (in module mldft.datagen.methods.density_fitting) get_L2_coulomb_matrix() (in module mldft.ofdft.basis_integrals) get_lebedev_grid() (in module mldft.utils.grids) get_local_frames_mesh_dict() (in module mldft.utils.visualize_3d) get_loss() (CoefficientLoss method) (EnergyGradientLoss method) (EnergyLoss method) (SingleLossFunction method) get_memory_usage_in_mb() (in module mldft.utils.multiprocess) get_mesh_kwargs() (LogMolecule method) get_metric_value() (in module mldft.utils.utils) get_mldft_data_path() (in module mldft.utils.environ) get_mldft_model_path() (in module mldft.utils.environ) get_molecule_dict() (LogMolecule method) get_n_atom_per_molecule() (OFData method) get_n_basis_per_molecule() (OFData method) get_normalization_vector() (in module mldft.ofdft.basis_integrals) get_nuclear_attraction_matrix() (in module mldft.ofdft.basis_integrals) get_nuclear_attraction_vector() (in module mldft.ofdft.basis_integrals) get_nuclear_gradient_matrix() (in module mldft.ofdft.basis_integrals) get_nuclear_gradient_vector() (in module mldft.ofdft.basis_integrals) get_num_molecules() (DataGenDataset method) (MiscXYZ method) (QM9 method) (QMUGS method) (SmallDataset method) get_optimizer_from_optimizer_args() (in module mldft.api.instantiate_from_args) get_overlap_matrix() (in module mldft.ofdft.basis_integrals) get_overlap_tensor() (in module mldft.ofdft.basis_integrals) get_overlapping_mean() (in module mldft.utils.plotting.summary_density_optimization) get_overlapping_quantiles() (in module mldft.utils.plotting.summary_density_optimization) get_path_from_environment_variable() (in module mldft.utils.environ) get_path_list_for_split_file() (in module mldft.utils.create_dataset_splits) get_pbar_str() (in module mldft.ofdft.optimizer) get_potential_vector() (in module mldft.ofdft.basis_integrals) get_qmugs_paths_and_group_ids() (in module mldft.utils.create_custom_splits) get_radial_densities() (in module mldft.utils.grids) get_rotation_matrix_from_basis() (in module mldft.utils.local_frames) get_runpath() (in module mldft.api.instantiate_from_args) get_runwise_density_optimization_data() (in module mldft.utils.plotting.summary_density_optimization) get_sample_from_mol() (SampleGenerator method) get_sample_generator_from_model_args() (in module mldft.api.instantiate_from_args) get_sample_overlap_matrix() (in module mldft.utils.overlap_matrices) get_sticks_mesh_dict() (in module mldft.utils.visualize_3d) get_vector_adam_optimizer() (in module mldft.api.instantiate_from_args) get_vw_functional() (FunctionalFactory class method) get_weights() (GroundStateOnlySampleWeigher method) (HasEnergyLabelSampleWeigher method) (InitialGuessOnlySampleWeigher method) (MinSCFIterationSampleWeigher method) (ProductSampleWeigher method) get_xyzfiles_from_base_args() (in module mldft.api.instantiate_from_args) getitem() (OFDataset method) GitInfo (class in mldft.utils.log_utils.hydra_callbacks) gradient_norm (BasicCallback attribute) gradient_norm_swarm_line_plot() (in module mldft.utils.plotting.summary_density_optimization) GRADIENT_STOPS_DECREASING (StoppingCriterion attribute) GradientDescent (class in mldft.ofdft.optimizer) Graphformer (class in mldft.ml.models.components.graphformer) grid (OFState attribute) grid_setup() (in module mldft.utils.grids) GroundStateOnlySampleWeigher (class in mldft.ml.models.components.sample_weighers)

H

hartree_functional() (in module mldft.ofdft.functional_factory) HasEnergyLabelSampleWeigher (class in mldft.ml.models.components.sample_weighers) hex_to_rgb() (in module mldft.ml.callbacks.mesh_logging)

HierarchicalPlotPDF (class in mldft.utils.pdf_utils) hueckel_guess() (in module mldft.ofdft.initial_guess) hueckel_guess_np() (in module mldft.ofdft.initial_guess)

I

id_to_chembl_conf_id() (QMUGS static method) init_lambda_z() (DimensionWiseRescaling method) initial_guess() (in module mldft.ofdft.density_optimization) InitialGuessDeltaModule (class in mldft.ml.models.components.initial_guess_delta_module) InitialGuessOnlySampleWeigher (class in mldft.ml.models.components.sample_weighers) initialize_energy_dicts() (in module mldft.utils.plotting.summary_density_optimization) initialize_transformation_matrices() (MasterTransformation static method) instantiate_callbacks() (in module mldft.utils.instantiators) instantiate_datamodule() (in module mldft.utils.instantiators)

instantiate_loggers() (in module mldft.utils.instantiators) instantiate_model() (in module mldft.utils.instantiators) integrals (BasisInfo attribute) invert_basis_transform() (MasterTransformation method) irreps_per_atom (BasisInfo attribute) is_numpy() (in module mldft.utils.coeffs_to_grid) is_subset() (BasisInfo method) is_torch() (in module mldft.utils.coeffs_to_grid) is_valid_label() (in module mldft.datagen.transform_dataset)

K

keys_recursive() (DatasetStatistics method) kohn_sham_data_dir (DataGenDataset attribute) (MiscXYZ attribute) (QM9 attribute) (SmallDataset attribute)

ksdft() (in module mldft.datagen.methods.ksdft_calculation) ksdft_density_matrix() (in module mldft.datagen.methods.density_fitting)

L

l_per_basis_func (BasisInfo attribute) l_per_shell (BasisInfo attribute) label_guess() (in module mldft.ofdft.initial_guess) leafs_only_override_dirname() (in module mldft.utils.omegaconf_resolvers) learning_rate (BasicCallback attribute) load_basis_from_zarr() (in module mldft.utils.molecules) load_charges_and_positions() (DataGenDataset method) (MiscXYZ method) (QM9 method) (QM9Test method) (QMUGS method) (SmallDataset method) load_charges_and_positions_sdf() (in module mldft.utils.molecules) load_molecule() (DataGenDataset method) (in module mldft.utils.draw_molecule) load_scf() (in module mldft.utils.molecules) load_statistic() (DatasetStatistics method) local_frames_from_positions() (in module mldft.utils.local_frames) local_frames_from_rel_positions() (in module mldft.utils.local_frames)

LocalBasisModule (class in mldft.ml.models.components.local_frames_module) LocalFramesModule (class in mldft.ml.models.components.local_frames_module) LocalFramesTransformMatrixDense (class in mldft.ml.models.components.local_frames_module) LocalFramesTransformMatrixSparse (class in mldft.ml.models.components.local_frames_module) locate_logging_mixins() (in module mldft.utils.log_utils.logging_mixin) log() (LoggingMixin method) (RankedLogger method) log_config() (in module mldft.api.cli_ofdft) log_config_text_to_tensorboard() (in module mldft.utils.log_utils.config_in_tensorboard) log_dict (LoggingMixin property) log_hyperparameters() (in module mldft.utils.log_utils.logging_utils) LogDistanceEmbeddings (class in mldft.ml.callbacks.image_logging) LoggingMixin (class in mldft.utils.log_utils.logging_mixin) LogGradientNorm (class in mldft.ml.callbacks.log_gradient_norm) LogGradientScatter (class in mldft.ml.callbacks.image_logging) LogMatplotlibToTensorboard (class in mldft.ml.callbacks.image_logging) LogMolecule (class in mldft.ml.callbacks.mesh_logging) LogParameterNorm (class in mldft.ml.callbacks.log_gradient_norm) LogTargetPredScatters (class in mldft.ml.callbacks.image_logging)

M

m_per_basis_func (BasisInfo attribute) m_per_shell (BasisInfo attribute) MAEEnergy (class in mldft.ml.models.components.training_metrics) MAEGradient (class in mldft.ml.models.components.training_metrics) MAEInitialGuess (class in mldft.ml.models.components.training_metrics) main() (in module mldft.api.cli_ofdft) (in module mldft.api.setup) (in module mldft.datagen.generate_labels_dataset) (in module mldft.datagen.kohn_sham_dataset) (in module mldft.datagen.transform_dataset) (in module mldft.ml.compute_dataset_statistics) (in module mldft.ml.train) (in module mldft.ofdft.run_density_optimization) MasterTransformation (class in mldft.ml.data.components.basis_transforms) message() (G3DLayer method) (G3DLayerTF method) (LocalBasisModule method) (ToyEnergy method) (ToyInitialGuessDelta method) minao_guess() (in module mldft.ofdft.initial_guess) minao_guess_np() (in module mldft.ofdft.initial_guess) minimal_sample_from_mol() (OFData class method) MinorSymLogLocator (class in mldft.utils.plotting.symlog_locater) MinSCFIterationSampleWeigher (class in mldft.ml.models.components.sample_weighers) MiscXYZ (class in mldft.datagen.datasets.misc) mldft.api module mldft.api.cli_ofdft module mldft.api.instantiate_from_args module mldft.api.setup module mldft.datagen module mldft.datagen.datasets module mldft.datagen.datasets.dataset module mldft.datagen.datasets.misc module mldft.datagen.datasets.qm9 module mldft.datagen.datasets.qmugs module mldft.datagen.datasets.small_dataset module mldft.datagen.datasets.two_electron_dataset module mldft.datagen.generate_labels_dataset module mldft.datagen.kohn_sham_dataset module mldft.datagen.methods module mldft.datagen.methods.density_fitting module mldft.datagen.methods.ksdft_calculation module mldft.datagen.methods.label_generation module mldft.datagen.methods.save_labels_in_zarr_file module mldft.datagen.transform_dataset module mldft.ml module mldft.ml.callbacks module mldft.ml.callbacks.base module mldft.ml.callbacks.checkpoint module mldft.ml.callbacks.custom_scalars module mldft.ml.callbacks.image_logging module mldft.ml.callbacks.log_gradient_norm module mldft.ml.callbacks.mesh_logging module mldft.ml.callbacks.print_overrides_callback module mldft.ml.callbacks.sub_model_summary module mldft.ml.callbacks.timing module mldft.ml.compute_dataset_statistics module mldft.ml.data module mldft.ml.data.components module mldft.ml.data.components.basis_info module mldft.ml.data.components.basis_transforms module mldft.ml.data.components.convert_transforms module mldft.ml.data.components.dataset module mldft.ml.data.components.loader module mldft.ml.data.components.of_batch module mldft.ml.data.components.of_data module mldft.ml.data.datamodule module mldft.ml.models module mldft.ml.models.components module mldft.ml.models.components.atom_ref module mldft.ml.models.components.density_coeff_embedding module mldft.ml.models.components.dimension_wise_rescaling module mldft.ml.models.components.g3d_layer module mldft.ml.models.components.g3d_layer_tf module mldft.ml.models.components.g3d_stack module mldft.ml.models.components.gbf_module module mldft.ml.models.components.graphformer module mldft.ml.models.components.initial_guess_delta_module module mldft.ml.models.components.local_frames_module module mldft.ml.models.components.loss_function module mldft.ml.models.components.mlp module mldft.ml.models.components.natural_reparametrization module mldft.ml.models.components.node_embedding module mldft.ml.models.components.sample_weighers module mldft.ml.models.components.shrink_gate_module module mldft.ml.models.components.toy_net module mldft.ml.models.components.training_metrics module mldft.ml.models.mldft_module module mldft.ml.preprocess module mldft.ml.preprocess.dataset_statistics module mldft.ml.train module mldft.ofdft module mldft.ofdft.basis_integrals module mldft.ofdft.callbacks module mldft.ofdft.density_optimization module mldft.ofdft.energies module mldft.ofdft.functional_factory module mldft.ofdft.initial_guess module mldft.ofdft.libxc_functionals module mldft.ofdft.ofstate module mldft.ofdft.optimizer module mldft.ofdft.plot_ofdft module mldft.ofdft.run_density_optimization module mldft.ofdft.torch_functionals module mldft.utils module mldft.utils.coeffs_to_grid module mldft.utils.conversions module mldft.utils.counter_file module mldft.utils.create_custom_splits module mldft.utils.create_dataset_splits module mldft.utils.create_subset module mldft.utils.cube_files module mldft.utils.download module

mldft.utils.draw_molecule module mldft.utils.einsum module mldft.utils.environ module mldft.utils.grids module mldft.utils.instantiators module mldft.utils.local_frames module mldft.utils.log_utils module mldft.utils.log_utils.config_in_tensorboard module mldft.utils.log_utils.hydra_callbacks module mldft.utils.log_utils.logging_mixin module mldft.utils.log_utils.logging_utils module mldft.utils.log_utils.pylogger module mldft.utils.lr_scheduling module mldft.utils.molecules module mldft.utils.multiprocess module mldft.utils.omegaconf_resolvers module mldft.utils.overlap_matrices module mldft.utils.pdf_utils module mldft.utils.plotting module mldft.utils.plotting.axes module mldft.utils.plotting.density_optimization module mldft.utils.plotting.limits module mldft.utils.plotting.plot_density_slices module mldft.utils.plotting.scatter module mldft.utils.plotting.summary_density_optimization module mldft.utils.plotting.symlog_locater module mldft.utils.pyscf_pretty_print module mldft.utils.rich_utils module mldft.utils.sad_guesser module mldft.utils.sparse module mldft.utils.utils module mldft.utils.visualize_3d module MLDFTLitModule (class in mldft.ml.models.mldft_module) MLP (class in mldft.ml.models.components.mlp) MLPStack (class in mldft.ml.models.components.graphformer) model (SampleGenerator attribute) model_config (SampleGenerator attribute) ModelCheckpointWithPermissions (class in mldft.ml.callbacks.checkpoint) ModelConfig (class in mldft.api.instantiate_from_args) module mldft.api mldft.api.cli_ofdft mldft.api.instantiate_from_args mldft.api.setup mldft.datagen mldft.datagen.datasets mldft.datagen.datasets.dataset mldft.datagen.datasets.misc mldft.datagen.datasets.qm9 mldft.datagen.datasets.qmugs mldft.datagen.datasets.small_dataset mldft.datagen.datasets.two_electron_dataset mldft.datagen.generate_labels_dataset mldft.datagen.kohn_sham_dataset mldft.datagen.methods mldft.datagen.methods.density_fitting mldft.datagen.methods.ksdft_calculation mldft.datagen.methods.label_generation mldft.datagen.methods.save_labels_in_zarr_file mldft.datagen.transform_dataset mldft.ml mldft.ml.callbacks mldft.ml.callbacks.base mldft.ml.callbacks.checkpoint mldft.ml.callbacks.custom_scalars mldft.ml.callbacks.image_logging mldft.ml.callbacks.log_gradient_norm mldft.ml.callbacks.mesh_logging mldft.ml.callbacks.print_overrides_callback mldft.ml.callbacks.sub_model_summary mldft.ml.callbacks.timing mldft.ml.compute_dataset_statistics mldft.ml.data mldft.ml.data.components mldft.ml.data.components.basis_info mldft.ml.data.components.basis_transforms mldft.ml.data.components.convert_transforms mldft.ml.data.components.dataset mldft.ml.data.components.loader mldft.ml.data.components.of_batch mldft.ml.data.components.of_data mldft.ml.data.datamodule mldft.ml.models mldft.ml.models.components mldft.ml.models.components.atom_ref mldft.ml.models.components.density_coeff_embedding mldft.ml.models.components.dimension_wise_rescaling mldft.ml.models.components.g3d_layer mldft.ml.models.components.g3d_layer_tf mldft.ml.models.components.g3d_stack mldft.ml.models.components.gbf_module mldft.ml.models.components.graphformer mldft.ml.models.components.initial_guess_delta_module mldft.ml.models.components.local_frames_module mldft.ml.models.components.loss_function mldft.ml.models.components.mlp mldft.ml.models.components.natural_reparametrization mldft.ml.models.components.node_embedding mldft.ml.models.components.sample_weighers mldft.ml.models.components.shrink_gate_module mldft.ml.models.components.toy_net mldft.ml.models.components.training_metrics mldft.ml.models.mldft_module mldft.ml.preprocess mldft.ml.preprocess.dataset_statistics mldft.ml.train mldft.ofdft mldft.ofdft.basis_integrals mldft.ofdft.callbacks mldft.ofdft.density_optimization mldft.ofdft.energies mldft.ofdft.functional_factory mldft.ofdft.initial_guess mldft.ofdft.libxc_functionals mldft.ofdft.ofstate mldft.ofdft.optimizer mldft.ofdft.plot_ofdft mldft.ofdft.run_density_optimization mldft.ofdft.torch_functionals mldft.utils mldft.utils.coeffs_to_grid mldft.utils.conversions mldft.utils.counter_file mldft.utils.create_custom_splits mldft.utils.create_dataset_splits mldft.utils.create_subset mldft.utils.cube_files mldft.utils.download mldft.utils.draw_molecule mldft.utils.einsum mldft.utils.environ mldft.utils.grids mldft.utils.instantiators mldft.utils.local_frames mldft.utils.log_utils mldft.utils.log_utils.config_in_tensorboard mldft.utils.log_utils.hydra_callbacks mldft.utils.log_utils.logging_mixin mldft.utils.log_utils.logging_utils mldft.utils.log_utils.pylogger mldft.utils.lr_scheduling mldft.utils.molecules mldft.utils.multiprocess mldft.utils.omegaconf_resolvers mldft.utils.overlap_matrices mldft.utils.pdf_utils mldft.utils.plotting mldft.utils.plotting.axes mldft.utils.plotting.density_optimization mldft.utils.plotting.limits mldft.utils.plotting.plot_density_slices mldft.utils.plotting.scatter mldft.utils.plotting.summary_density_optimization mldft.utils.plotting.symlog_locater mldft.utils.pyscf_pretty_print mldft.utils.rich_utils mldft.utils.sad_guesser mldft.utils.sparse mldft.utils.utils mldft.utils.visualize_3d mol (BasicCallback attribute) (Energies attribute) (OFState attribute) mol_to_str() (in module mldft.utils.pyscf_pretty_print) mole_to_sum_formula() (in module mldft.utils.pyscf_pretty_print) molecules (SmallDataset attribute) monkey_patch_pyscf_mol_str() (in module mldft.utils.pyscf_pretty_print)

N

n_atom (OFData attribute) n_basis (BasisInfo property) (OFData attribute) n_basis_per_atom (OFData attribute) n_electron (OFData attribute) n_shells (BasisInfo property) n_shells_per_atom (BasisInfo attribute) n_types (BasisInfo property) name (DataGenDataset attribute) (MiscXYZ attribute) (QM9 attribute) (SmallDataset attribute)

natural_reparametrization_matrices() (in module mldft.ml.models.components.natural_reparametrization) natural_reparametrization_matrices_torch() (in module mldft.ml.models.components.natural_reparametrization) negative_integrated_density_penalty_weight (SampleGenerator attribute) NegativeIntegratedDensity (class in mldft.ofdft.functional_factory) NodeEmbedding (class in mldft.ml.models.components.node_embedding) NONE (SADNormalizationMode attribute) nr_rks() (in module mldft.ofdft.libxc_functionals) nuclear_attraction_functional() (in module mldft.ofdft.functional_factory) num_molecules (DataGenDataset attribute) (SmallDataset attribute) num_processes (DataGenDataset attribute) (SmallDataset attribute)

O

OFBatch (class in mldft.ml.data.components.of_batch) OFCollater (class in mldft.ml.data.components.of_batch) OFData (class in mldft.ml.data.components.of_data) OFDataModule (class in mldft.ml.data.datamodule) OFDataset (class in mldft.ml.data.components.dataset) OFDFTRunResult (class in mldft.api.cli_ofdft) OFLoader (class in mldft.ml.data.components.loader) OFState (class in mldft.ofdft.ofstate) on_before_optimizer_step() (LogGradientNorm method) (LogParameterNorm method) on_fit_start() (AddMetricAndLossCustomScalars method) (PrintOverrides method) on_multirun_end() (AnyRunCallback method) on_multirun_start() (AnyRunCallback method) on_run_end() (AnyRunCallback method) on_run_start() (AnyRunCallback method)

on_test_epoch_end() (MLDFTLitModule method) on_train_batch_end() (OnStepCallbackWithTiming method) on_train_epoch_end() (MLDFTLitModule method) on_train_start() (MLDFTLitModule method) on_validation_batch_end() (OnStepCallbackWithTiming method) on_validation_epoch_end() (MLDFTLitModule method) on_validation_epoch_start() (MLDFTLitModule method) OnStepCallbackWithTiming (class in mldft.ml.callbacks.base) optimize() (GradientDescent method) (Optimizer method) (SLSQP method) (TorchOptimizer method) (TrustRegionConstrained method) (VectorAdam method) Optimizer (class in mldft.ofdft.optimizer) OptimizerConfig (class in mldft.api.instantiate_from_args)

P

parameter_norm() (in module mldft.ml.callbacks.log_gradient_norm) parse_args() (in module mldft.utils.draw_molecule) parse_field_info() (DatasetStatisticsFitter static method) parse_field_name() (DatasetStatisticsFitter static method) parse_reps_import() (in module mldft.utils.omegaconf_resolvers) parse_run_path() (in module mldft.ofdft.run_density_optimization) patched_extrapolate() (in module mldft.datagen.methods.ksdft_calculation) path_to_basename() (in module mldft.utils.omegaconf_resolvers) PER_ATOM_SIMPLE (SADNormalizationMode attribute) PER_ATOM_WEIGHTED (SADNormalizationMode attribute) PER_MOLECULE_SIMPLE (SADNormalizationMode attribute) PER_MOLECULE_WEIGHTED (SADNormalizationMode attribute) PerBasisFuncShrinkGateModule (class in mldft.ml.models.components.shrink_gate_module) PerSampleAbsoluteErrorMetric (class in mldft.ml.models.components.training_metrics) PerSampleWeightedPerCoeffLossFunction (class in mldft.ml.models.components.loss_function) PerSampleWeightedPerSampleLossFunction (class in mldft.ml.models.components.loss_function) perturb_fock_matrix() (in module mldft.datagen.methods.ksdft_calculation) perturbed_label_guess() (in module mldft.ofdft.initial_guess) plot_density() (in module mldft.utils.visualize_3d) plot_density_optimization() (in module mldft.utils.plotting.density_optimization) plot_density_optimization_trajectory_means() (in module mldft.utils.plotting.summary_density_optimization)

plot_distance_embeddings() (Graphformer method) plot_energy_summary_scatter() (in module mldft.utils.plotting.summary_density_optimization) plot_from_dir() (in module mldft.ofdft.plot_ofdft) plot_mean_and_fill_between() (in module mldft.utils.plotting.summary_density_optimization) plot_molecule() (in module mldft.utils.visualize_3d) plot_ofdft_energy_distribution() (in module mldft.utils.plotting.summary_density_optimization) plot_ofdft_run_summary() (in module mldft.utils.plotting.summary_density_optimization) plot_orbital() (in module mldft.utils.visualize_3d) plot_quantiles_data() (in module mldft.utils.plotting.summary_density_optimization) plotting_worker() (in module mldft.ofdft.run_density_optimization) predict_dataloader() (OFDataModule method) print_basis() (in module mldft.utils.molecules) print_config_tree() (in module mldft.utils.rich_utils) PrintOverrides (class in mldft.ml.callbacks.print_overrides_callback) ProductSampleWeigher (class in mldft.ml.models.components.sample_weighers) proj_minao_guess() (in module mldft.ofdft.initial_guess) project_gradient() (in module mldft.ml.models.components.loss_function) project_gradient_difference() (in module mldft.ml.models.components.loss_function) ProjectGradient (class in mldft.ml.data.components.convert_transforms) pyscf_to_e3nn_local_frames_matrix() (in module mldft.utils.local_frames) pyscf_to_e3nn_matrix() (in module mldft.utils.local_frames) pyscf_to_rdkit() (in module mldft.utils.conversions)

Q

QM9 (class in mldft.datagen.datasets.qm9) QM9Test (class in mldft.datagen.datasets.qm9) QMUGS (class in mldft.datagen.datasets.qmugs)

QMUGSBin (class in mldft.datagen.datasets.qmugs) QMUGSLargeBins (class in mldft.datagen.datasets.qmugs) query_yes_no() (in module mldft.api.setup)

R

RankedLogger (class in mldft.utils.log_utils.pylogger) raw_data_dir (DataGenDataset attribute) (MiscXYZ attribute) (QM9 attribute) (SmallDataset attribute) read_xyz_file() (in module mldft.utils.molecules) remove_broken_files() (in module mldft.datagen.transform_dataset) Representation (class in mldft.ml.data.components.of_data) required_derivative() (in module mldft.ofdft.libxc_functionals) requires_grid() (in module mldft.ofdft.functional_factory) (in module mldft.ofdft.libxc_functionals) rescale_coeffs_and_gradient() (DimensionWiseRescaling method) reset_parameters() (G3DLayer method) (G3DLayerTF method) (NodeEmbedding method)

rich_to_str() (in module mldft.utils.rich_utils) rotate_molecule2_onto_plane() (in module mldft.utils.plotting.plot_density_slices) rotate_molecule_pca() (in module mldft.utils.plotting.plot_density_slices) run_ksdft_and_handle_exceptions() (in module mldft.datagen.kohn_sham_dataset) run_label_generation() (in module mldft.datagen.generate_labels_dataset) run_labelgen_task() (in module mldft.datagen.generate_labels_dataset) run_ofdft() (in module mldft.api.cli_ofdft) (in module mldft.ofdft.run_density_optimization) run_ofdft_from_components() (in module mldft.api.cli_ofdft) run_singlepoint_ofdft() (in module mldft.ofdft.run_density_optimization) run_to_checkpoint_path() (in module mldft.ofdft.run_density_optimization)

S

SADGuesser (class in mldft.utils.sad_guesser) SADNormalizationMode (class in mldft.utils.sad_guesser) sample_forward() (AtomRef method) (LocalFramesTransformMatrixDense method) (LocalFramesTransformMatrixSparse method) (MLDFTLitModule method) (SimpleQuadraticAtomRef method) sample_weights_to_atom_weights() (in module mldft.ml.preprocess.dataset_statistics) sample_weights_to_basis_function_weights() (in module mldft.ml.preprocess.dataset_statistics) SampleGenerator (class in mldft.ofdft.run_density_optimization) save_config() (in module mldft.datagen.kohn_sham_dataset) save_dataset_info() (in module mldft.datagen.generate_labels_dataset) save_density_fitted_data() (in module mldft.datagen.methods.save_labels_in_zarr_file) save_density_optimization_metrics() (in module mldft.utils.plotting.summary_density_optimization) save_sample() (in module mldft.api.cli_ofdft) save_statistic() (DatasetStatistics method) save_to() (DatasetStatistics method) save_to_file() (BasicCallback method) savefig() (HierarchicalPlotPDF method) scipy_functional() (in module mldft.ofdft.optimizer) set_default_torch_dtype() (in module mldft.utils.utils) set_equal_aspect_and_square_limits() (in module mldft.utils.plotting.limits) set_general_options() (in module mldft.utils.draw_molecule) set_num_threads() (in module mldft.utils.multiprocess) set_torch_defaults_worker() (in module mldft.ofdft.run_density_optimization) setup() (MLDFTLitModule method) (OFDataModule method) shell_beginning_mask (BasisInfo attribute)

shell_to_first_basis_func (BasisInfo attribute) ShrinkGateModule (class in mldft.ml.models.components.shrink_gate_module) SimpleQuadraticAtomRef (class in mldft.ml.models.components.atom_ref) SingleLossFunction (class in mldft.ml.models.components.loss_function) slash_to_backslash() (in module mldft.utils.omegaconf_resolvers) SLSQP (class in mldft.ofdft.optimizer) SmallDataset (class in mldft.datagen.datasets.small_dataset) smart_override_dirname() (in module mldft.utils.omegaconf_resolvers) smooth_falloff() (in module mldft.ml.models.components.node_embedding) split_by_atom() (in module mldft.ml.data.components.convert_transforms) split_field_by_atom() (OFData method) split_field_by_atom_type() (BasisInfo method) split_non_grouped() (in module mldft.utils.create_dataset_splits) split_overrides_string() (in module mldft.utils.omegaconf_resolvers) SplitByAtom (class in mldft.ml.data.components.convert_transforms) stopping_index_line_plot() (in module mldft.utils.plotting.summary_density_optimization) StoppingCriterion (class in mldft.ofdft.ofstate) str_to_torch_float_dtype() (in module mldft.ml.data.components.convert_transforms) StrEnumwithCheck (class in mldft.ml.data.components.of_data) SubModelSummary (class in mldft.ml.callbacks.sub_model_summary) subsample_swarm() (in module mldft.utils.plotting.summary_density_optimization) sum (Energies property) summarize() (SubModelSummary method) summary_string() (GroundStateOnlySampleWeigher method) (HasEnergyLabelSampleWeigher method) (InitialGuessOnlySampleWeigher method) (MinSCFIterationSampleWeigher method) (ProductSampleWeigher method)

T

task_wrapper() (in module mldft.utils.utils) tensorboard_logger (MLDFTLitModule property) test_dataloader() (OFDataModule method) test_step() (MLDFTLitModule method) tick_values() (MinorSymLogLocator method) to_numpy() (in module mldft.ml.data.components.convert_transforms) to_pyvista() (DataCube method) to_torch() (in module mldft.ml.data.components.convert_transforms) ToGlobalNatRep (class in mldft.ml.data.components.basis_transforms) ToLocalFrames (class in mldft.ml.data.components.basis_transforms) ToNumpy (class in mldft.ml.data.components.convert_transforms) torch_functional() (in module mldft.ofdft.torch_functionals) TorchOptimizer (class in mldft.ofdft.optimizer) total_energy (Energies property) ToTorch (class in mldft.ml.data.components.convert_transforms)

ToyEnergy (class in mldft.ml.models.components.toy_net) ToyInitialGuessDelta (class in mldft.ml.models.components.toy_net) ToyNet (class in mldft.ml.models.components.toy_net) train_dataloader() (OFDataModule method) training_step() (MLDFTLitModule method) transform_coeffs_to_local() (in module mldft.utils.local_frames) transform_dataset() (in module mldft.datagen.transform_dataset) transform_local_coeffs_to_global() (in module mldft.utils.local_frames) transform_tensor() (in module mldft.ml.data.components.basis_transforms) transform_tensor_with_sample() (in module mldft.ml.data.components.basis_transforms) transforms (SampleGenerator attribute) translate_check_xc() (in module mldft.ofdft.libxc_functionals) translate_xc_code() (in module mldft.ofdft.libxc_functionals) tree_to_string() (in module mldft.utils.log_utils.config_in_tensorboard) TrustRegionConstrained (class in mldft.ofdft.optimizer) TwoElectronDataset (class in mldft.datagen.datasets.two_electron_dataset)

U

unpack_args_for_imap() (in module mldft.utils.multiprocess) update() (MAEEnergy method) (MAEGradient method) (MAEInitialGuess method)

update_with_errors() (PerSampleAbsoluteErrorMetric method)

V

val_dataloader() (OFDataModule method) validation_step() (MLDFTLitModule method) values_only_override_dirname() (in module mldft.utils.omegaconf_resolvers)

VectorAdam (class in mldft.ofdft.optimizer) verify_files() (DataGenDataset method) visualize_density() (in module mldft.utils.visualize_3d) visualize_orbital() (in module mldft.utils.visualize_3d)

W

weigh_loss() (PerSampleWeightedPerCoeffLossFunction method) (PerSampleWeightedPerSampleLossFunction method) (SingleLossFunction method)

WeightedLoss (class in mldft.ml.models.components.loss_function) worker() (in module mldft.ofdft.run_density_optimization) worker_init_fn() (in module mldft.ml.data.datamodule) write_file() (in module mldft.utils.draw_molecule)