API

• Alchemy
  • mbeAlchemyScale
    • mbeAlchemyScale
      • mbeAlchemyScale.scale()
• Analysis
  • gdml_mat52
    • gdml_mat52()
  • gdml_mat52_wrk
    • gdml_mat52_wrk()
  • RDF
    • RDF
      • RDF.run()
  • ProblematicStructures
    • ProblematicStructures
      • ProblematicStructures.course_n_cl_e
      • ProblematicStructures.course_n_cl_r
      • ProblematicStructures.find()
      • ProblematicStructures.get_pd()
      • ProblematicStructures.kwargs_subplot
      • ProblematicStructures.loss_func
      • ProblematicStructures.loss_func_kwargs
      • ProblematicStructures.n_cl_samples()
      • ProblematicStructures.plot_annotate_cl_idx
      • ProblematicStructures.plot_cl_losses()
      • ProblematicStructures.plot_lolli_color
      • ProblematicStructures.prob_cl_indices()
      • ProblematicStructures.refine_min_r_ratio
      • ProblematicStructures.refine_n_cl
      • ProblematicStructures.select_prob_indices()
• Data sets
  • DataSet
    • DataSet.E
    • DataSet.E_max
    • DataSet.E_mean
    • DataSet.E_min
    • DataSet.E_var
    • DataSet.F
    • DataSet.F_max
    • DataSet.F_mean
    • DataSet.F_min
    • DataSet.F_var
    • DataSet.asdict()
    • DataSet.comp_ids
    • DataSet.convertE()
    • DataSet.convertF()
    • DataSet.convertR()
    • DataSet.e_unit
    • DataSet.entity_ids
    • DataSet.load()
    • DataSet.mb
    • DataSet.mb_dsets_md5
    • DataSet.mb_models_md5
    • DataSet.md5
    • DataSet.name
    • DataSet.print()
    • DataSet.r_prov_ids
    • DataSet.r_prov_specs
    • DataSet.theory
    • DataSet.write_xyz()
• Descriptors
  • com_distance_sum
    • com_distance_sum()
  • Criteria
    • Criteria
      • Criteria.accept()
  • max_atom_pair_dist
    • max_atom_pair_dist()
• GDML
  • Descriptor
    • Desc
      • Desc
    • _from_r
      • _from_r()
    • _pbc_diff
      • _pbc_diff()
    • _pdist
      • _pdist()
    • _r_to_desc
      • _r_to_desc()
    • _r_to_d_desc
      • _r_to_d_desc()
  • Training
    • add_valid_errors
      • add_valid_errors()
    • Analytic
      • Analytic
    • GDMLTrain
      • GDMLTrain
    • get_test_idxs
      • get_test_idxs()
    • Iterative
      • Iterative
    • model_errors
      • model_errors()
    • _assemble_kernel_mat_wkr
      • _assemble_kernel_mat_wkr()
  • Symmetries
    • bipartite_match
      • bipartite_match()
    • complete_sym_group
      • complete_sym_group()
    • find_perms
      • find_perms()
    • inv_perm
      • inv_perm()
    • salvage_subgroup
      • salvage_subgroup()
    • sync_perm_mat
      • sync_perm_mat()
    • to_cycles
      • to_cycles()
    • _bipartite_match_wkr
      • _bipartite_match_wkr()
  • Predictions
    • GDMLPredict
      • GDMLPredict
    • _predict_wkr
      • _predict_wkr()
  • Sample
    • draw_strat_sample
      • draw_strat_sample()
• Interfaces
  • ASE
    • mbeCalculator
      • mbeCalculator.calculate()
      • mbeCalculator.implemented_properties
• Logger
  • GDMLLogger
    • GDMLLogger
      • GDMLLogger.log_model()
      • GDMLLogger.t_start()
      • GDMLLogger.t_stop()
  • set_log_level
    • set_log_level()
• Losses
  • loss_f_mse
    • loss_f_mse()
  • loss_f_rmse
    • loss_f_rmse()
  • loss_f_e_weighted_mse
    • loss_f_e_weighted_mse()
  • mae
    • mae()
  • mse
    • mse()
  • rmse
    • rmse()
  • sse
    • sse()
• MBE
  • decomp_to_total
    • decomp_to_total()
  • gen_r_entity_combs
    • gen_r_entity_combs()
  • gen_r_idxs_worker
    • gen_r_idxs_worker()
  • mbe_contrib
    • mbe_contrib()
  • mbePredict
    • mbePredict
      • mbePredict.box_scaling_type
      • mbePredict.compute_nbody()
      • mbePredict.compute_nbody_decomp()
      • mbePredict.finite_diff_dh
      • mbePredict.get_avail_entities()
      • mbePredict.only_normal_stress
      • mbePredict.periodic_cell
      • mbePredict.predict()
      • mbePredict.predict_decomp()
      • mbePredict.use_voigt
      • mbePredict.virial_form
  • mbe_worker
    • mbe_worker()
• Models
  • gapModel
    • gapModel
  • gdmlModel
    • gdmlModel
      • gdmlModel.add_modifications()
      • gdmlModel.code_version
      • gdmlModel.md5
      • gdmlModel.save()
  • schnetModel
    • schnetModel
  • Model
    • Model
      • Model.md5
      • Model.nbody_order
• Prediction Sets
  • PredictSet
    • PredictSet.E_true
    • PredictSet.F_true
    • PredictSet.asdict()
    • PredictSet.comp_ids
    • PredictSet.e_unit
    • PredictSet.entity_ids
    • PredictSet.load()
    • PredictSet.load_dataset()
    • PredictSet.load_models()
    • PredictSet.name
    • PredictSet.nbody_predictions()
    • PredictSet.prepare()
    • PredictSet.theory
• Periodic
  • Cell
    • Cell
      • Cell.cell_v
      • Cell.d_mic()
      • Cell.r_mic()
      • Cell.volume
• Predictors
  • predict_gap
    • predict_gap()
  • predict_gap_decomp
    • predict_gap_decomp()
  • predict_gdml
    • predict_gdml()
  • predict_gdml_decomp
    • predict_gdml_decomp()
  • predict_schnet
    • predict_schnet()
  • predict_schnet_decomp
    • predict_schnet_decomp()
  • _predict_gdml_wkr
    • _predict_gdml_wkr()
• Stress
  • to_voigt
    • to_voigt()
  • virial_atom_loop
    • virial_atom_loop()
  • virial_finite_diff
    • virial_finite_diff()
• Structure generation
  • packmol_gen
    • get_packmol_input
      • get_packmol_input()
    • run_packmol
      • run_packmol()
  • utils
    • mol_to_mass_fractions
      • mol_to_mass_fractions()
    • get_mixture_density
      • get_mixture_density()
    • get_shape_volume
      • get_shape_volume()
    • get_num_mols
      • get_num_mols()
• Switching functions
  • linear_switching
    • linear_switching()
• Training
  • mbGDMLTrain
    • mbGDMLTrain
      • mbGDMLTrain.active_train()
      • mbGDMLTrain.bayes_opt()
      • mbGDMLTrain.bayes_opt_n_check_rising
      • mbGDMLTrain.bayes_opt_params
      • mbGDMLTrain.bayes_opt_params_final
      • mbGDMLTrain.check_energy_pred
      • mbGDMLTrain.create_task()
      • mbGDMLTrain.grid_search()
      • mbGDMLTrain.keep_tasks
      • mbGDMLTrain.loss_func
      • mbGDMLTrain.loss_kwargs
      • mbGDMLTrain.min_memory_analytic()
      • mbGDMLTrain.plot_bayes_opt_gp()
      • mbGDMLTrain.require_E_eval
      • mbGDMLTrain.save_idxs()
      • mbGDMLTrain.save_valid_csv()
      • mbGDMLTrain.sigma_bounds
      • mbGDMLTrain.sigma_grid
      • mbGDMLTrain.test_model()
      • mbGDMLTrain.train_model()
• Utilities
  • atoms_by_element
    • atoms_by_element()
  • atoms_by_number
    • atoms_by_number()
  • center_structures
    • center_structures()
  • chunk_array
    • chunk_array()
  • chunk_iterable
    • chunk_iterable()
  • convert_forces
    • convert_forces()
  • gen_combs
    • gen_combs()
  • get_comp_ids
    • get_comp_ids()
  • get_filename
    • get_filename()
  • get_files
    • get_files()
  • get_entity_ids
    • get_entity_ids()
  • get_R_slice
    • get_R_slice()
  • md5_data
    • md5_data()
  • parse_xyz
    • parse_xyz()
  • save_json
    • save_json()
  • string_xyz_arrays
    • string_xyz_arrays()
  • write_xyz
    • write_xyz()