Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W _ _assemble_kernel_mat() (mbgdml._gdml.train.GDMLTrain method) _assemble_kernel_mat_wkr() (in module mbgdml._gdml.train) _bipartite_match_wkr() (in module mbgdml._gdml.perm) _from_r() (in module mbgdml._gdml.desc) _pbc_diff() (in module mbgdml._gdml.desc) _pdist() (in module mbgdml._gdml.desc) _predict_gdml_wkr() (in module mbgdml.predictors.gdml_predict) _predict_wkr() (in module mbgdml._gdml.predict) _r_to_d_desc() (in module mbgdml._gdml.desc) _r_to_desc() (in module mbgdml._gdml.desc) _recov_int_const() (mbgdml._gdml.train.GDMLTrain method) _set_bulk_mp() (mbgdml._gdml.predict.GDMLPredict method) _set_chunk_size() (mbgdml._gdml.predict.GDMLPredict method) _set_num_workers() (mbgdml._gdml.predict.GDMLPredict method) A accept() (mbgdml.descriptors.Criteria method) active_train() (mbgdml.train.mbGDMLTrain method) add_modifications() (mbgdml.models.gdmlModel method) add_valid_errors() (in module mbgdml._gdml.train) Analytic (class in mbgdml._gdml.solvers.analytic) asdict() (mbgdml.data.DataSet method) (mbgdml.data.PredictSet method) atoms_by_element() (in module mbgdml.utils) atoms_by_number() (in module mbgdml.utils) B bayes_opt() (mbgdml.train.mbGDMLTrain method) bayes_opt_n_check_rising (mbgdml.train.mbGDMLTrain attribute) bayes_opt_params (mbgdml.train.mbGDMLTrain attribute) bayes_opt_params_final (mbgdml.train.mbGDMLTrain attribute) bipartite_match() (in module mbgdml._gdml.perm) box_scaling_type (mbgdml.mbe.mbePredict attribute) C calculate() (mbgdml.interfaces.ase.mbeCalculator method) Cell (class in mbgdml.periodic) cell_v (mbgdml.periodic.Cell property) center_structures() (in module mbgdml.utils) check_energy_pred (mbgdml.train.mbGDMLTrain attribute) chunk_array() (in module mbgdml.utils) chunk_iterable() (in module mbgdml.utils) code_version (mbgdml.models.gdmlModel property) com_distance_sum() (in module mbgdml.descriptors) comp_ids (mbgdml.data.DataSet property) (mbgdml.data.PredictSet property) complete_sym_group() (in module mbgdml._gdml.perm) compute_nbody() (mbgdml.mbe.mbePredict method) compute_nbody_decomp() (mbgdml.mbe.mbePredict method) convert_forces() (in module mbgdml.utils) convertE() (mbgdml.data.DataSet method) convertF() (mbgdml.data.DataSet method) convertR() (mbgdml.data.DataSet method) course_n_cl_e (mbgdml.analysis.problematic.ProblematicStructures attribute) course_n_cl_r (mbgdml.analysis.problematic.ProblematicStructures attribute) Covalent fragments create_model() (mbgdml._gdml.train.GDMLTrain method) create_task() (mbgdml._gdml.train.GDMLTrain method) (mbgdml.train.mbGDMLTrain method) Criteria (class in mbgdml.descriptors) D d_desc_from_comp() (mbgdml._gdml.desc.Desc method) d_desc_to_comp() (mbgdml._gdml.desc.Desc method) d_mic() (mbgdml.periodic.Cell method) DataSet (class in mbgdml.data) decomp_to_total() (in module mbgdml.mbe) Desc (class in mbgdml._gdml.desc) draw_strat_sample() (in module mbgdml._gdml.sample) E E (mbgdml.data.DataSet property) E_max (mbgdml.data.DataSet property) E_mean (mbgdml.data.DataSet property) E_min (mbgdml.data.DataSet property) E_true (mbgdml.data.PredictSet property) e_unit (mbgdml.data.DataSet property) (mbgdml.data.PredictSet property) E_var (mbgdml.data.DataSet property) entity_ids (mbgdml.data.DataSet property) (mbgdml.data.PredictSet property) F F (mbgdml.data.DataSet property) F_max (mbgdml.data.DataSet property) F_mean (mbgdml.data.DataSet property) F_min (mbgdml.data.DataSet property) F_true (mbgdml.data.PredictSet property) F_var (mbgdml.data.DataSet property) find() (mbgdml.analysis.problematic.ProblematicStructures method) find_perms() (in module mbgdml._gdml.perm) finite_diff_dh (mbgdml.mbe.mbePredict attribute) from_R() (mbgdml._gdml.desc.Desc method) G gapModel (class in mbgdml.models) gdml_mat52() (in module mbgdml.analysis.models) gdml_mat52_wrk() (in module mbgdml.analysis.models) GDMLLogger (class in mbgdml.logger) gdmlModel (class in mbgdml.models) GDMLPredict (class in mbgdml._gdml.predict) GDMLTrain (class in mbgdml._gdml.train) gen_combs() (in module mbgdml.utils) gen_r_entity_combs() (in module mbgdml.mbe) gen_r_idxs_worker() (in module mbgdml.mbe) get_avail_entities() (mbgdml.mbe.mbePredict method) get_comp_ids() (in module mbgdml.utils) get_entity_ids() (in module mbgdml.utils) get_filename() (in module mbgdml.utils) get_files() (in module mbgdml.utils) get_GPU_batch() (mbgdml._gdml.predict.GDMLPredict method) get_mixture_density() (in module mbgdml.structure_gen.utils) get_num_mols() (in module mbgdml.structure_gen.utils) get_packmol_input() (in module mbgdml.structure_gen.packmol_gen) get_pd() (mbgdml.analysis.problematic.ProblematicStructures method) get_R_slice() (in module mbgdml.utils) get_shape_volume() (in module mbgdml.structure_gen.utils) get_test_idxs() (in module mbgdml._gdml.train) grid_search() (mbgdml.train.mbGDMLTrain method) I implemented_properties (mbgdml.interfaces.ase.mbeCalculator attribute) Intersecting fragments inv_perm() (in module mbgdml._gdml.perm) Iterative (class in mbgdml._gdml.solvers.iterative) K keep_tasks (mbgdml.train.mbGDMLTrain attribute) kwargs_subplot (mbgdml.analysis.problematic.ProblematicStructures attribute) L linear_switching() (in module mbgdml.switching) load() (mbgdml.data.DataSet method) (mbgdml.data.PredictSet method) load_dataset() (mbgdml.data.PredictSet method) load_models() (mbgdml.data.PredictSet method) log_model() (mbgdml.logger.GDMLLogger method) loss_f_e_weighted_mse() (in module mbgdml.losses) loss_f_mse() (in module mbgdml.losses) loss_f_rmse() (in module mbgdml.losses) loss_func (mbgdml.analysis.problematic.ProblematicStructures attribute) (mbgdml.train.mbGDMLTrain attribute) loss_func_kwargs (mbgdml.analysis.problematic.ProblematicStructures attribute) loss_kwargs (mbgdml.train.mbGDMLTrain attribute) M mae() (in module mbgdml.losses) max_atom_pair_dist() (in module mbgdml.descriptors) mb (mbgdml.data.DataSet property) mb_dsets_md5 (mbgdml.data.DataSet property) mb_models_md5 (mbgdml.data.DataSet property) mbe_contrib() (in module mbgdml.mbe) mbe_worker() (in module mbgdml.mbe) mbeAlchemyScale (class in mbgdml.alchemy) mbeCalculator (class in mbgdml.interfaces.ase) mbePredict (class in mbgdml.mbe) mbGDMLTrain (class in mbgdml.train) md5 (mbgdml.data.DataSet property) (mbgdml.models.gdmlModel property) (mbgdml.models.Model attribute) md5_data() (in module mbgdml.utils) min_memory_analytic() (mbgdml.train.mbGDMLTrain method) Model (class in mbgdml.models) model_errors() (in module mbgdml._gdml.train) mol_to_mass_fractions() (in module mbgdml.structure_gen.utils) mse() (in module mbgdml.losses) N n_cl_samples() (mbgdml.analysis.problematic.ProblematicStructures method) name (mbgdml.data.DataSet property) (mbgdml.data.PredictSet attribute) nbody_order (mbgdml.models.Model attribute) nbody_predictions() (mbgdml.data.PredictSet method) O only_normal_stress (mbgdml.mbe.mbePredict attribute) P parse_xyz() (in module mbgdml.utils) periodic_cell (mbgdml.mbe.mbePredict property) perm() (mbgdml._gdml.desc.Desc static method) plot_annotate_cl_idx (mbgdml.analysis.problematic.ProblematicStructures attribute) plot_bayes_opt_gp() (mbgdml.train.mbGDMLTrain method) plot_cl_losses() (mbgdml.analysis.problematic.ProblematicStructures method) plot_lolli_color (mbgdml.analysis.problematic.ProblematicStructures attribute) predict() (mbgdml._gdml.predict.GDMLPredict method) (mbgdml.mbe.mbePredict method) predict_decomp() (mbgdml.mbe.mbePredict method) predict_gap() (in module mbgdml.predictors) predict_gap_decomp() (in module mbgdml.predictors) predict_gdml() (in module mbgdml.predictors) predict_gdml_decomp() (in module mbgdml.predictors) predict_schnet() (in module mbgdml.predictors) predict_schnet_decomp() (in module mbgdml.predictors) PredictSet (class in mbgdml.data) prepare() (mbgdml.data.PredictSet method) prepare_parallel() (mbgdml._gdml.predict.GDMLPredict method) print() (mbgdml.data.DataSet method) prob_cl_indices() (mbgdml.analysis.problematic.ProblematicStructures method) ProblematicStructures (class in mbgdml.analysis.problematic) R r_mic() (mbgdml.periodic.Cell method) r_prov_ids (mbgdml.data.DataSet property) r_prov_specs (mbgdml.data.DataSet property) RDF (class in mbgdml.analysis.rdf) refine_min_r_ratio (mbgdml.analysis.problematic.ProblematicStructures attribute) refine_n_cl (mbgdml.analysis.problematic.ProblematicStructures attribute) require_E_eval (mbgdml.train.mbGDMLTrain attribute) rmse() (in module mbgdml.losses) run() (mbgdml.analysis.rdf.RDF method) run_packmol() (in module mbgdml.structure_gen.packmol_gen) S salvage_subgroup() (in module mbgdml._gdml.perm) save() (mbgdml.models.gdmlModel method) save_idxs() (mbgdml.train.mbGDMLTrain method) save_json() (in module mbgdml.utils) save_valid_csv() (mbgdml.train.mbGDMLTrain method) scale() (mbgdml.alchemy.mbeAlchemyScale method) schnetModel (class in mbgdml.models) select_prob_indices() (mbgdml.analysis.problematic.ProblematicStructures method) set_alphas() (mbgdml._gdml.predict.GDMLPredict method) set_log_level() (in module mbgdml.logger) set_R_d_desc() (mbgdml._gdml.predict.GDMLPredict method) set_R_desc() (mbgdml._gdml.predict.GDMLPredict method) sigma_bounds (mbgdml.train.mbGDMLTrain attribute) sigma_grid (mbgdml.train.mbGDMLTrain attribute) solve() (mbgdml._gdml.solvers.analytic.Analytic method) (mbgdml._gdml.solvers.iterative.Iterative method) sse() (in module mbgdml.losses) string_xyz_arrays() (in module mbgdml.utils) sync_perm_mat() (in module mbgdml._gdml.perm) T t_start() (mbgdml.logger.GDMLLogger method) t_stop() (mbgdml.logger.GDMLLogger method) test_model() (mbgdml.train.mbGDMLTrain method) theory (mbgdml.data.DataSet property) (mbgdml.data.PredictSet property) to_cycles() (in module mbgdml._gdml.perm) to_voigt() (in module mbgdml.stress) train() (mbgdml._gdml.train.GDMLTrain method) train_labels() (mbgdml._gdml.train.GDMLTrain method) train_model() (mbgdml.train.mbGDMLTrain method) U use_voigt (mbgdml.mbe.mbePredict attribute) V virial_atom_loop() (in module mbgdml.stress) virial_finite_diff() (in module mbgdml.stress) virial_form (mbgdml.mbe.mbePredict attribute) volume (mbgdml.periodic.Cell property) W write_xyz() (in module mbgdml.utils) (mbgdml.data.DataSet method)