API Documentation

• Cluster Expansion Settings
  • Concentration
    • Concentration.__init__()
    • Concentration.add_usr_defined_eq_constraints()
    • Concentration.add_usr_defined_ineq_constraints()
    • Concentration.clease_objtype
    • Concentration.conc_in_int()
    • Concentration.from_dict()
    • Concentration.get_conc_max_component()
    • Concentration.get_conc_min_component()
    • Concentration.get_concentration_vector()
    • Concentration.get_individual_comp_range()
    • Concentration.get_random_concentration()
    • Concentration.is_valid()
    • Concentration.is_valid_conc()
    • Concentration.load()
    • Concentration.save()
    • Concentration.set_conc_formula_unit()
    • Concentration.set_conc_ranges()
    • Concentration.to_float_conc()
    • Concentration.todict()
    • Concentration.trivial_bounds
  • ClusterExpansionSettings
    • ClusterExpansionSettings.ARG_KEYS
    • ClusterExpansionSettings.KWARG_KEYS
    • ClusterExpansionSettings.OTHER_KEYS
    • ClusterExpansionSettings.__init__()
    • ClusterExpansionSettings.all_cf_names
    • ClusterExpansionSettings.all_elements
    • ClusterExpansionSettings.atomic_concentration_ratio
    • ClusterExpansionSettings.atoms
    • ClusterExpansionSettings.background_indices
    • ClusterExpansionSettings.basis_func_type
    • ClusterExpansionSettings.basis_functions
    • ClusterExpansionSettings.clear_cache()
    • ClusterExpansionSettings.clease_objtype
    • ClusterExpansionSettings.cluster_list
    • ClusterExpansionSettings.cluster_mng
    • ClusterExpansionSettings.clusters_table()
    • ClusterExpansionSettings.connect()
    • ClusterExpansionSettings.create_cluster_list_and_trans_matrix()
    • ClusterExpansionSettings.db_name
    • ClusterExpansionSettings.ensure_clusters_exist()
    • ClusterExpansionSettings.from_dict()
    • ClusterExpansionSettings.get_active_sublattices()
    • ClusterExpansionSettings.get_all_figures_as_atoms()
    • ClusterExpansionSettings.get_all_templates()
    • ClusterExpansionSettings.get_bg_syms()
    • ClusterExpansionSettings.get_cluster_corresponding_to_cf_name()
    • ClusterExpansionSettings.get_prim_cell_id()
    • ClusterExpansionSettings.get_sublattice_site_ratios()
    • ClusterExpansionSettings.ignore_background_atoms
    • ClusterExpansionSettings.ignored_species_and_conc
    • ClusterExpansionSettings.include_background_atoms
    • ClusterExpansionSettings.index_by_basis
    • ClusterExpansionSettings.index_by_sublattice
    • ClusterExpansionSettings.load()
    • ClusterExpansionSettings.max_cluster_dia
    • ClusterExpansionSettings.max_cluster_size
    • ClusterExpansionSettings.multiplicity_factor
    • ClusterExpansionSettings.non_background_indices
    • ClusterExpansionSettings.num_active_sublattices
    • ClusterExpansionSettings.num_basis
    • ClusterExpansionSettings.num_cf
    • ClusterExpansionSettings.num_elements
    • ClusterExpansionSettings.num_unique_elements
    • ClusterExpansionSettings.prepare_new_active_template()
    • ClusterExpansionSettings.prim_cell
    • ClusterExpansionSettings.ref_index_trans_symm
    • ClusterExpansionSettings.requires_build()
    • ClusterExpansionSettings.save()
    • ClusterExpansionSettings.set_active_template()
    • ClusterExpansionSettings.size
    • ClusterExpansionSettings.skew_threshold
    • ClusterExpansionSettings.spin_dict
    • ClusterExpansionSettings.supercell_factor
    • ClusterExpansionSettings.template_atoms
    • ClusterExpansionSettings.todict()
    • ClusterExpansionSettings.trans_matrix
    • ClusterExpansionSettings.unique_element_without_background()
    • ClusterExpansionSettings.unique_elements
    • ClusterExpansionSettings.view_clusters()
    • ClusterExpansionSettings.view_templates()
  • CEBulk()
  • CECrystal()
  • CESlab()
  • settings_from_json()
• Structure Generation
  • NewStructures
    • NewStructures.__init__()
    • NewStructures.connect()
    • NewStructures.num_in_gen()
    • NewStructures.num_to_gen()
    • NewStructures.generate_probe_structure()
    • NewStructures.corr_func_table_name
    • NewStructures.generate_gs_structure_multiple_templates()
    • NewStructures.generate_gs_structure()
    • NewStructures.generate_random_structures()
    • NewStructures.generate_one_random_structure()
    • NewStructures.generate_initial_pool()
    • NewStructures.generate_conc_extrema()
    • NewStructures.generate_metropolis_trajectory()
    • NewStructures.insert_structures()
    • NewStructures.insert_structure()
  • MaxAttemptReachedError
• Basis Functions
  • Polynomial
    • Polynomial.name
    • Polynomial.get_spin_dict()
    • Polynomial.get_basis_functions()
  • Trigonometric
    • Trigonometric.name
    • Trigonometric.get_spin_dict()
    • Trigonometric.get_basis_functions()
  • BinaryLinear
    • BinaryLinear.name
    • BinaryLinear.__init__()
    • BinaryLinear.get_spin_dict()
    • BinaryLinear.get_basis_functions()
    • BinaryLinear.customize_full_cluster_name()
    • BinaryLinear.todict()
  • BasisFunction
    • BasisFunction.name
    • BasisFunction.__init__()
    • BasisFunction.unique_elements
    • BasisFunction.num_unique_elements
    • BasisFunction.spin_dict
    • BasisFunction.basis_functions
    • BasisFunction.get_spin_dict()
    • BasisFunction.get_basis_functions()
    • BasisFunction.customize_full_cluster_name()
    • BasisFunction.todict()
    • BasisFunction.clease_objtype
    • BasisFunction.load()
    • BasisFunction.save()
• Correlation Functions
  • CorrFunction
    • CorrFunction.__init__()
    • CorrFunction.settings
    • CorrFunction.connect()
    • CorrFunction.get_cf()
    • CorrFunction.get_cf_by_names()
    • CorrFunction.reconfigure_single_db_entry()
    • CorrFunction.cf_table_name
    • CorrFunction.clear_cf_table()
    • CorrFunction.reconfigure_db_entries()
    • CorrFunction.iter_reconfigure_db_entries()
    • CorrFunction.reconfigure_inconsistent_cf_table_entries()
    • CorrFunction.check_consistency_of_cf_table_entries()
    • CorrFunction.set_template()
  • ClusterNotTrackedError
• Fitting ECIs
  • The Evaluate Class
    • Evaluate
      • Evaluate.__init__()
      • Evaluate.set_normalization()
      • Evaluate.scoring_scheme
      • Evaluate.concentrations
      • Evaluate.default_select_cond
      • Evaluate.set_fitting_scheme()
      • Evaluate.fit_required()
      • Evaluate.fit()
      • Evaluate.get_eci()
      • Evaluate.get_eci_dict()
      • Evaluate.load_eci_dict()
      • Evaluate.load_eci()
      • Evaluate.save_eci()
      • Evaluate.plot_fit()
      • Evaluate.atomic_concentrations
      • Evaluate.alpha_CV()
      • Evaluate.cv_for_alpha()
      • Evaluate.cv_scores
      • Evaluate.plot_CV()
      • Evaluate.plot_ECI()
      • Evaluate.mae()
      • Evaluate.rmse()
      • Evaluate.loocv_fast()
      • Evaluate.loocv()
      • Evaluate.k_fold_cv()
      • Evaluate.generalization_error()
      • Evaluate.export_dataset()
      • Evaluate.get_cv_score()
      • Evaluate.get_energy_predict()
      • Evaluate.get_energy_true()
      • Evaluate.get_eci_by_size()
      • Evaluate.print_coverage_report()
  • Fitting ECI’s to Non-Energy Properties
• Fitting Schemes
  • LinearRegression
    • LinearRegression.__init__()
    • LinearRegression.weight_matrix
    • LinearRegression.fit()
    • LinearRegression.precision_matrix()
    • LinearRegression.get_instance_array()
    • LinearRegression.is_scalar()
    • LinearRegression.get_scalar_parameter()
    • LinearRegression.support_fast_loocv
  • Tikhonov
    • Tikhonov.__init__()
    • Tikhonov.fit()
    • Tikhonov.precision_matrix()
    • Tikhonov.get_instance_array()
    • Tikhonov.is_scalar()
    • Tikhonov.get_scalar_parameter()
  • Lasso
    • Lasso.__init__()
    • Lasso.max_iter
    • Lasso.fit()
    • Lasso.weight_matrix
    • Lasso.get_instance_array()
    • Lasso.is_scalar()
    • Lasso.get_scalar_parameter()
    • Lasso.precision_matrix()
    • Lasso.support_fast_loocv
  • GAFit
    • GAFit.__init__()
    • GAFit.get_eci()
    • GAFit.design_matrix()
    • GAFit.fit_individual()
    • GAFit.evaluate_fitness()
    • GAFit.flip_one_mutation()
    • GAFit.make_valid()
    • GAFit.create_new_generation()
    • GAFit.mutate()
    • GAFit.population_diversity()
    • GAFit.best_individual
    • GAFit.num_data
    • GAFit.best_individual_indx
    • GAFit.index_of_selected_clusters()
    • GAFit.save_population()
    • GAFit.plot_evolution()
    • GAFit.run()
    • GAFit.check_valid()
  • PhysicalRidge
    • PhysicalRidge.__init__()
    • PhysicalRidge.add_constraint()
    • PhysicalRidge.fit_data()
    • PhysicalRidge.size_decay
    • PhysicalRidge.dia_decay
    • PhysicalRidge.sizes_from_names()
    • PhysicalRidge.diameters_from_names()
    • PhysicalRidge.fit()
  • BayesianCompressiveSensing
    • BayesianCompressiveSensing.__init__()
    • BayesianCompressiveSensing.precision_matrix()
    • BayesianCompressiveSensing.mu()
    • BayesianCompressiveSensing.optimal_gamma()
    • BayesianCompressiveSensing.optimal_lamb()
    • BayesianCompressiveSensing.optimal_inv_variance()
    • BayesianCompressiveSensing.optimal_shape_lamb()
    • BayesianCompressiveSensing.update_quantities()
    • BayesianCompressiveSensing.selected
    • BayesianCompressiveSensing.update_sigma_mu()
    • BayesianCompressiveSensing.get_basis_function_index()
    • BayesianCompressiveSensing.log_likelihood_for_each_gamma()
    • BayesianCompressiveSensing.rmse()
    • BayesianCompressiveSensing.num_ecis
    • BayesianCompressiveSensing.todict()
    • BayesianCompressiveSensing.save()
    • BayesianCompressiveSensing.load()
    • BayesianCompressiveSensing.estimate_loocv()
    • BayesianCompressiveSensing.fit()
    • BayesianCompressiveSensing.show_shape_parameter()
    • BayesianCompressiveSensing.weight_matrix
  • SequentialClusterRidge
    • SequentialClusterRidge.__init__()
    • SequentialClusterRidge.fit()
• Monte Carlo
  • Canonical MC
    • Montecarlo
      • Montecarlo.NAME
      • Montecarlo.__init__()
      • Montecarlo.update_current_energy()
      • Montecarlo.reset()
      • Montecarlo.reset_averagers()
      • Montecarlo.add_bias()
      • Montecarlo.attach()
      • Montecarlo.iter_observers()
      • Montecarlo.initialize_run()
      • Montecarlo.run()
      • Montecarlo.irun()
      • Montecarlo.meta_info
      • Montecarlo.current_accept_rate
      • Montecarlo.get_thermodynamic_quantities()
      • Montecarlo.count_atoms()
      • Montecarlo.execute_observers()
  • Semi-grand canonical MC
    • SGCMonteCarlo
      • SGCMonteCarlo.__init__()
      • SGCMonteCarlo.observe_singlets
      • SGCMonteCarlo.reset()
      • SGCMonteCarlo.calc
      • SGCMonteCarlo.settings
      • SGCMonteCarlo.chemical_potential
      • SGCMonteCarlo.reset_eci()
      • SGCMonteCarlo.run()
      • SGCMonteCarlo.singlet2composition()
      • SGCMonteCarlo.reset_averagers()
      • SGCMonteCarlo.get_thermodynamic_quantities()
  • Related Objects
    • BaseMC
      • BaseMC.__init__()
      • BaseMC.evaluator
      • BaseMC.atoms
      • BaseMC.temperature
      • BaseMC.T
    • MCStep
      • MCStep.step
      • MCStep.energy
      • MCStep.move_accepted
      • MCStep.last_move
      • MCStep.other
      • MCStep.move_rejected
      • MCStep.__init__()
      • MCStep.clease_objtype
      • MCStep.load()
      • MCStep.save()
    • Monte Carlo Constraints
      • MCConstraint
        • MCConstraint.name
      • ConstrainSwapByBasis
        • ConstrainSwapByBasis.__init__()
      • ConstrainElementInserts
        • ConstrainElementInserts.__init__()
      • FixedElement
        • FixedElement.__init__()
      • CollectiveVariableConstraint
        • CollectiveVariableConstraint.__init__()
      • PairConstraint
        • PairConstraint.__init__()
      • FixedIndices
        • FixedIndices.__init__()
        • FixedIndices.name
    • Monte Carlo Observers
      • MCObserver
        • MCObserver.calculate_from_scratch()
        • MCObserver.get_averages()
        • MCObserver.interval_ok()
        • MCObserver.name
        • MCObserver.observe_step()
        • MCObserver.reset()
      • SGCObserver
        • SGCObserver.__init__()
        • SGCObserver.counter
        • SGCObserver.energy
        • SGCObserver.energy_sq
        • SGCObserver.get_current_energy()
        • SGCObserver.interval_ok()
        • SGCObserver.name
        • SGCObserver.observe_step()
        • SGCObserver.reset()
        • SGCObserver.singl_eng
        • SGCObserver.singlets
      • CorrelationFunctionObserver
        • CorrelationFunctionObserver.__init__()
        • CorrelationFunctionObserver.get_averages()
        • CorrelationFunctionObserver.name
        • CorrelationFunctionObserver.reset()
      • Snapshot
        • Snapshot.__init__()
        • Snapshot.close()
        • Snapshot.name
      • EnergyEvolution
        • EnergyEvolution.__init__()
        • EnergyEvolution.name
        • EnergyEvolution.reset()
        • EnergyEvolution.save()
      • LowestEnergyStructure
        • LowestEnergyStructure.__init__()
        • LowestEnergyStructure.calc
        • LowestEnergyStructure.emin_results
        • LowestEnergyStructure.energy
        • LowestEnergyStructure.lowest_energy
        • LowestEnergyStructure.name
        • LowestEnergyStructure.observe_step()
        • LowestEnergyStructure.reset()
      • DiffractionObserver
        • DiffractionObserver.__init__()
        • DiffractionObserver.get_averages()
        • DiffractionObserver.interval_ok()
        • DiffractionObserver.reset()
      • EnergyPlotUpdater
        • EnergyPlotUpdater.__init__()
        • EnergyPlotUpdater.name
      • ConcentrationObserver
        • ConcentrationObserver.__init__()
        • ConcentrationObserver.calculate_from_scratch()
        • ConcentrationObserver.get_averages()
        • ConcentrationObserver.interval_ok()
        • ConcentrationObserver.name
        • ConcentrationObserver.new_concentration()
        • ConcentrationObserver.observe_step()
        • ConcentrationObserver.reset()
      • SiteOrderParameter
        • SiteOrderParameter.__init__()
        • SiteOrderParameter.get_averages()
        • SiteOrderParameter.interval_ok()
        • SiteOrderParameter.name
        • SiteOrderParameter.reset()
      • MultiStateSGCConcObserver
        • MultiStateSGCConcObserver.__init__()
        • MultiStateSGCConcObserver.get_averages()
        • MultiStateSGCConcObserver.name
        • MultiStateSGCConcObserver.reset()
      • SGCState
        • SGCState.__init__()
        • SGCState.prefix
        • SGCState.reset()
      • EntropyProductionRate
        • EntropyProductionRate.__init__()
        • EntropyProductionRate.flush_buffer()
        • EntropyProductionRate.reset()
        • EntropyProductionRate.update()
      • AcceptanceRate
        • AcceptanceRate.__init__()
        • AcceptanceRate.get_averages()
        • AcceptanceRate.rate
        • AcceptanceRate.reset()
      • MoveObserver
        • MoveObserver.__init__()
        • MoveObserver.interval_ok()
        • MoveObserver.observe_step()
        • MoveObserver.reconstruct()
        • MoveObserver.reconstruct_iter()
        • MoveObserver.reset()
    • Monte Carlo Evaluator
      • An Example
      • The API
        • MCEvaluator
          • MCEvaluator.__init__()
          • MCEvaluator.atoms
          • MCEvaluator.get_energy()
          • MCEvaluator.reset()
          • MCEvaluator.apply_system_changes()
          • MCEvaluator.undo_system_changes()
          • MCEvaluator.keep_system_changes()
          • MCEvaluator.get_energy_given_change()
          • MCEvaluator.synchronize()
    • Trial Move Generators
      • The API
        • TrialMoveGenerator
          • TrialMoveGenerator.__init__()
          • TrialMoveGenerator.initialize()
          • TrialMoveGenerator.remove_constraints()
          • TrialMoveGenerator.name
          • TrialMoveGenerator.add_constraint()
          • TrialMoveGenerator.get_single_trial_move()
          • TrialMoveGenerator.get_trial_move()
          • TrialMoveGenerator.on_move_accepted()
          • TrialMoveGenerator.on_move_rejected()
        • SingleTrialMoveGenerator
          • SingleTrialMoveGenerator.CHANGE_NAME
          • SingleTrialMoveGenerator.__init__()
          • SingleTrialMoveGenerator.name_matches()
          • SingleTrialMoveGenerator.made_changes()
        • RandomFlip
          • RandomFlip.CHANGE_NAME
          • RandomFlip.__init__()
          • RandomFlip.get_single_trial_move()
        • RandomSwap
          • RandomSwap.CHANGE_NAME
          • RandomSwap.__init__()
          • RandomSwap.get_single_trial_move()
          • RandomSwap.on_move_accepted()
          • RandomSwap.is_tracked()
        • MixedSwapFlip
          • MixedSwapFlip.__init__()
          • MixedSwapFlip.generators
          • MixedSwapFlip.weights
          • MixedSwapFlip.initialize()
          • MixedSwapFlip.get_single_trial_move()
          • MixedSwapFlip.on_move_accepted()
          • MixedSwapFlip.on_move_rejected()
        • RandomFlipWithinBasis
          • RandomFlipWithinBasis.CHANGE_NAME
          • RandomFlipWithinBasis.__init__()
          • RandomFlipWithinBasis.get_single_trial_move()
• Getting Data From Database
  • InconsistentDataError
  • DataManager
    • DataManager.__init__()
    • DataManager.get_data()
    • DataManager.to_csv()
    • DataManager.get_matching_names()
    • DataManager.get_cols()
    • DataManager.groups()
  • CorrFuncEnergyDataManager
    • CorrFuncEnergyDataManager.__init__()
    • CorrFuncEnergyDataManager.get_data()
  • CorrelationFunctionGetter
    • CorrelationFunctionGetter.__init__()
    • CorrelationFunctionGetter.names
    • CorrelationFunctionGetter.get_property()
  • CorrFuncVolumeDataManager
    • CorrFuncVolumeDataManager.__init__()
    • CorrFuncVolumeDataManager.get_data()
  • CorrelationFunctionGetterVolDepECI
    • CorrelationFunctionGetterVolDepECI.__init__()
    • CorrelationFunctionGetterVolDepECI.build()
    • CorrelationFunctionGetterVolDepECI.get_data()
    • CorrelationFunctionGetterVolDepECI.groups()
  • FinalStructPropertyGetter
    • FinalStructPropertyGetter.__init__()
    • FinalStructPropertyGetter.name
    • FinalStructPropertyGetter.get_property()
  • make_corr_func_data_manager()
• Geometry Tools
  • max_sphere_dia_in_cell()
  • supercell_which_contains_sphere()
  • cell_wall_distances()
• Post Process Plotting
  • plot_fit()
  • plot_fit_residual()
  • plot_eci()
  • plot_cv()
  • plot_convex_hull()