Index

_

__init__() (clease.basis_function.BasisFunction method) (clease.basis_function.BinaryLinear method) (clease.corr_func.CorrFunction method) (clease.data_manager.CorrelationFunctionGetter method) (clease.data_manager.CorrelationFunctionGetterVolDepECI method) (clease.data_manager.CorrFuncEnergyDataManager method) (clease.data_manager.CorrFuncVolumeDataManager method) (clease.data_manager.DataManager method) (clease.data_manager.FinalStructPropertyGetter method) (clease.datastructures.mc_step.MCStep method) (clease.evaluate.Evaluate method) (clease.montecarlo.base.BaseMC method) (clease.montecarlo.constraints.CollectiveVariableConstraint method) (clease.montecarlo.constraints.ConstrainElementInserts method) (clease.montecarlo.constraints.ConstrainSwapByBasis method) (clease.montecarlo.constraints.FixedElement method) (clease.montecarlo.constraints.FixedIndices method) (clease.montecarlo.constraints.PairConstraint method) (clease.montecarlo.mc_evaluator.MCEvaluator method) (clease.montecarlo.montecarlo.Montecarlo method) (clease.montecarlo.observers.AcceptanceRate method) (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.CorrelationFunctionObserver method) (clease.montecarlo.observers.DiffractionObserver method) (clease.montecarlo.observers.EnergyEvolution method) (clease.montecarlo.observers.EnergyPlotUpdater method) (clease.montecarlo.observers.EntropyProductionRate method) (clease.montecarlo.observers.LowestEnergyStructure method) (clease.montecarlo.observers.MoveObserver method) (clease.montecarlo.observers.MultiStateSGCConcObserver method) (clease.montecarlo.observers.SGCObserver method) (clease.montecarlo.observers.SGCState method) (clease.montecarlo.observers.SiteOrderParameter method) (clease.montecarlo.observers.Snapshot method) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) (clease.montecarlo.trial_move_generator.MixedSwapFlip method) (clease.montecarlo.trial_move_generator.RandomFlip method) (clease.montecarlo.trial_move_generator.RandomFlipWithinBasis method) (clease.montecarlo.trial_move_generator.RandomSwap method) (clease.montecarlo.trial_move_generator.SingleTrialMoveGenerator method) (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) (clease.regression.ga_fit.GAFit method) (clease.regression.Lasso method) (clease.regression.LinearRegression method) (clease.regression.physical_ridge.PhysicalRidge method) (clease.regression.sequential_cluster_ridge.SequentialClusterRidge method) (clease.regression.Tikhonov method) (clease.settings.ClusterExpansionSettings method) (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) (clease.structgen.new_struct.NewStructures method)

A

AcceptanceRate (class in clease.montecarlo.observers) add_bias() (clease.montecarlo.montecarlo.Montecarlo method) add_constraint() (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) (clease.regression.physical_ridge.PhysicalRidge method) add_usr_defined_eq_constraints() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) add_usr_defined_ineq_constraints() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) all_cf_names (clease.settings.ClusterExpansionSettings property)

all_elements (clease.settings.ClusterExpansionSettings property) alpha_CV() (clease.evaluate.Evaluate method) apply_system_changes() (clease.montecarlo.mc_evaluator.MCEvaluator method) ARG_KEYS (clease.settings.ClusterExpansionSettings attribute) atomic_concentration_ratio (clease.settings.ClusterExpansionSettings property) atomic_concentrations (clease.evaluate.Evaluate property) atoms (clease.montecarlo.base.BaseMC property) (clease.montecarlo.mc_evaluator.MCEvaluator property) (clease.settings.ClusterExpansionSettings property) attach() (clease.montecarlo.montecarlo.Montecarlo method)

B

background_indices (clease.settings.ClusterExpansionSettings property) BaseMC (class in clease.montecarlo.base) basis_func_type (clease.settings.ClusterExpansionSettings property) basis_functions (clease.basis_function.BasisFunction property) (clease.settings.ClusterExpansionSettings property)

BasisFunction (class in clease.basis_function) BayesianCompressiveSensing (class in clease.regression.bayesian_compressive_sensing) best_individual (clease.regression.ga_fit.GAFit property) best_individual_indx (clease.regression.ga_fit.GAFit property) BinaryLinear (class in clease.basis_function) build() (clease.data_manager.CorrelationFunctionGetterVolDepECI method)

C

calc (clease.montecarlo.observers.LowestEnergyStructure property) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo property) calculate_from_scratch() (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.MCObserver method) CEBulk() (in module clease.settings) CECrystal() (in module clease.settings) cell_wall_distances() (in module clease.geometry) CESlab() (in module clease.settings) cf_table_name (clease.corr_func.CorrFunction property) CHANGE_NAME (clease.montecarlo.trial_move_generator.RandomFlip attribute) (clease.montecarlo.trial_move_generator.RandomFlipWithinBasis attribute) (clease.montecarlo.trial_move_generator.RandomSwap attribute) (clease.montecarlo.trial_move_generator.SingleTrialMoveGenerator attribute) check_consistency_of_cf_table_entries() (clease.corr_func.CorrFunction method) check_valid() (clease.regression.ga_fit.GAFit method) chemical_potential (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo property) clear_cache() (clease.settings.ClusterExpansionSettings method) clear_cf_table() (clease.corr_func.CorrFunction method) clease.corr_func module clease.data_manager module clease.geometry module clease.montecarlo.constraints module clease.montecarlo.observers module clease.plot_post_process module clease.settings module clease.settings.concentration module clease.structgen.new_struct module clease.tools module

clease_objtype (clease.basis_function.BasisFunction attribute) (clease.datastructures.mc_step.MCStep attribute) (clease.settings.ClusterExpansionSettings attribute) (clease.settings.Concentration attribute) (clease.settings.concentration.Concentration attribute) close() (clease.montecarlo.observers.Snapshot method) cluster_list (clease.settings.ClusterExpansionSettings property) cluster_mng (clease.settings.ClusterExpansionSettings property) ClusterExpansionSettings (class in clease.settings) ClusterNotTrackedError clusters_table() (clease.settings.ClusterExpansionSettings method) CollectiveVariableConstraint (class in clease.montecarlo.constraints) conc_in_int() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) Concentration (class in clease.settings) (class in clease.settings.concentration) ConcentrationObserver (class in clease.montecarlo.observers) concentrations (clease.evaluate.Evaluate property) connect() (clease.corr_func.CorrFunction method) (clease.settings.ClusterExpansionSettings method) (clease.structgen.new_struct.NewStructures method) ConstrainElementInserts (class in clease.montecarlo.constraints) ConstrainSwapByBasis (class in clease.montecarlo.constraints) corr_func_table_name (clease.structgen.new_struct.NewStructures property) CorrelationFunctionGetter (class in clease.data_manager) CorrelationFunctionGetterVolDepECI (class in clease.data_manager) CorrelationFunctionObserver (class in clease.montecarlo.observers) CorrFuncEnergyDataManager (class in clease.data_manager) CorrFunction (class in clease.corr_func) CorrFuncVolumeDataManager (class in clease.data_manager) count_atoms() (clease.montecarlo.montecarlo.Montecarlo method) counter (clease.montecarlo.observers.SGCObserver property) create_cluster_list_and_trans_matrix() (clease.settings.ClusterExpansionSettings method) create_new_generation() (clease.regression.ga_fit.GAFit method) current_accept_rate (clease.montecarlo.montecarlo.Montecarlo property) customize_full_cluster_name() (clease.basis_function.BasisFunction method) (clease.basis_function.BinaryLinear method) cv_for_alpha() (clease.evaluate.Evaluate method) cv_scores (clease.evaluate.Evaluate property)

D

DataManager (class in clease.data_manager) db_name (clease.settings.ClusterExpansionSettings property) default_select_cond (clease.evaluate.Evaluate property)

design_matrix() (clease.regression.ga_fit.GAFit method) dia_decay (clease.regression.physical_ridge.PhysicalRidge property) diameters_from_names() (clease.regression.physical_ridge.PhysicalRidge method) DiffractionObserver (class in clease.montecarlo.observers)

E

emin_results (clease.montecarlo.observers.LowestEnergyStructure property) energy (clease.datastructures.mc_step.MCStep attribute) (clease.montecarlo.observers.LowestEnergyStructure property) (clease.montecarlo.observers.SGCObserver property) energy_sq (clease.montecarlo.observers.SGCObserver property) EnergyEvolution (class in clease.montecarlo.observers) EnergyPlotUpdater (class in clease.montecarlo.observers)

ensure_clusters_exist() (clease.settings.ClusterExpansionSettings method) EntropyProductionRate (class in clease.montecarlo.observers) estimate_loocv() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) Evaluate (class in clease.evaluate) evaluate_fitness() (clease.regression.ga_fit.GAFit method) evaluator (clease.montecarlo.base.BaseMC property) execute_observers() (clease.montecarlo.montecarlo.Montecarlo method) export_dataset() (clease.evaluate.Evaluate method)

F

FinalStructPropertyGetter (class in clease.data_manager) fit() (clease.evaluate.Evaluate method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) (clease.regression.Lasso method) (clease.regression.LinearRegression method) (clease.regression.physical_ridge.PhysicalRidge method) (clease.regression.sequential_cluster_ridge.SequentialClusterRidge method) (clease.regression.Tikhonov method) fit_data() (clease.regression.physical_ridge.PhysicalRidge method)

fit_individual() (clease.regression.ga_fit.GAFit method) fit_required() (clease.evaluate.Evaluate method) FixedElement (class in clease.montecarlo.constraints) FixedIndices (class in clease.montecarlo.constraints) flip_one_mutation() (clease.regression.ga_fit.GAFit static method) flush_buffer() (clease.montecarlo.observers.EntropyProductionRate method) from_dict() (clease.settings.ClusterExpansionSettings class method) (clease.settings.Concentration class method) (clease.settings.concentration.Concentration class method)

G

GAFit (class in clease.regression.ga_fit) generalization_error() (clease.evaluate.Evaluate method) generate_conc_extrema() (clease.structgen.new_struct.NewStructures method) generate_gs_structure() (clease.structgen.new_struct.NewStructures method) generate_gs_structure_multiple_templates() (clease.structgen.new_struct.NewStructures method) generate_initial_pool() (clease.structgen.new_struct.NewStructures method) generate_metropolis_trajectory() (clease.structgen.new_struct.NewStructures method) generate_one_random_structure() (clease.structgen.new_struct.NewStructures method) generate_probe_structure() (clease.structgen.new_struct.NewStructures method) generate_random_structures() (clease.structgen.new_struct.NewStructures method) generators (clease.montecarlo.trial_move_generator.MixedSwapFlip property) get_active_sublattices() (clease.settings.ClusterExpansionSettings method) get_all_figures_as_atoms() (clease.settings.ClusterExpansionSettings method) get_all_templates() (clease.settings.ClusterExpansionSettings method) get_averages() (clease.montecarlo.observers.AcceptanceRate method) (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.CorrelationFunctionObserver method) (clease.montecarlo.observers.DiffractionObserver method) (clease.montecarlo.observers.MCObserver method) (clease.montecarlo.observers.MultiStateSGCConcObserver method) (clease.montecarlo.observers.SiteOrderParameter method) get_basis_function_index() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) get_basis_functions() (clease.basis_function.BasisFunction method) (clease.basis_function.BinaryLinear method) (clease.basis_function.Polynomial method) (clease.basis_function.Trigonometric method) get_bg_syms() (clease.settings.ClusterExpansionSettings method) get_cf() (clease.corr_func.CorrFunction method) get_cf_by_names() (clease.corr_func.CorrFunction method) get_cluster_corresponding_to_cf_name() (clease.settings.ClusterExpansionSettings method) get_cols() (clease.data_manager.DataManager method) get_conc_max_component() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) get_conc_min_component() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) get_concentration_vector() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) get_current_energy() (clease.montecarlo.observers.SGCObserver method) get_cv_score() (clease.evaluate.Evaluate method) get_data() (clease.data_manager.CorrelationFunctionGetterVolDepECI method) (clease.data_manager.CorrFuncEnergyDataManager method) (clease.data_manager.CorrFuncVolumeDataManager method) (clease.data_manager.DataManager method)

get_eci() (clease.evaluate.Evaluate method) (clease.regression.ga_fit.GAFit method) get_eci_by_size() (clease.evaluate.Evaluate method) get_eci_dict() (clease.evaluate.Evaluate method) get_energy() (clease.montecarlo.mc_evaluator.MCEvaluator method) get_energy_given_change() (clease.montecarlo.mc_evaluator.MCEvaluator method) get_energy_predict() (clease.evaluate.Evaluate method) get_energy_true() (clease.evaluate.Evaluate method) get_individual_comp_range() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) get_instance_array() (clease.regression.Lasso static method) (clease.regression.LinearRegression method) (clease.regression.Tikhonov static method) get_matching_names() (clease.data_manager.DataManager method) get_prim_cell_id() (clease.settings.ClusterExpansionSettings method) get_property() (clease.data_manager.CorrelationFunctionGetter method) (clease.data_manager.FinalStructPropertyGetter method) get_random_concentration() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) get_scalar_parameter() (clease.regression.Lasso method) (clease.regression.LinearRegression method) (clease.regression.Tikhonov method) get_single_trial_move() (clease.montecarlo.trial_move_generator.MixedSwapFlip method) (clease.montecarlo.trial_move_generator.RandomFlip method) (clease.montecarlo.trial_move_generator.RandomFlipWithinBasis method) (clease.montecarlo.trial_move_generator.RandomSwap method) (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) get_spin_dict() (clease.basis_function.BasisFunction method) (clease.basis_function.BinaryLinear method) (clease.basis_function.Polynomial method) (clease.basis_function.Trigonometric method) get_sublattice_site_ratios() (clease.settings.ClusterExpansionSettings method) get_thermodynamic_quantities() (clease.montecarlo.montecarlo.Montecarlo method) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) get_trial_move() (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) groups() (clease.data_manager.CorrelationFunctionGetterVolDepECI method) (clease.data_manager.DataManager method)

I

ignore_background_atoms (clease.settings.ClusterExpansionSettings property) ignored_species_and_conc (clease.settings.ClusterExpansionSettings property) include_background_atoms (clease.settings.ClusterExpansionSettings property) InconsistentDataError index_by_basis (clease.settings.ClusterExpansionSettings property) index_by_sublattice (clease.settings.ClusterExpansionSettings property) index_of_selected_clusters() (clease.regression.ga_fit.GAFit method) initialize() (clease.montecarlo.trial_move_generator.MixedSwapFlip method) (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) initialize_run() (clease.montecarlo.montecarlo.Montecarlo method) insert_structure() (clease.structgen.new_struct.NewStructures method) insert_structures() (clease.structgen.new_struct.NewStructures method) interval_ok() (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.DiffractionObserver method) (clease.montecarlo.observers.MCObserver method) (clease.montecarlo.observers.MoveObserver method) (clease.montecarlo.observers.SGCObserver method) (clease.montecarlo.observers.SiteOrderParameter method)

irun() (clease.montecarlo.montecarlo.Montecarlo method) is_scalar() (clease.regression.Lasso method) (clease.regression.LinearRegression method) (clease.regression.Tikhonov method) is_tracked() (clease.montecarlo.trial_move_generator.RandomSwap method) is_valid() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) is_valid_conc() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) iter_observers() (clease.montecarlo.montecarlo.Montecarlo method) iter_reconfigure_db_entries() (clease.corr_func.CorrFunction method)

K

k_fold_cv() (clease.evaluate.Evaluate method)

keep_system_changes() (clease.montecarlo.mc_evaluator.MCEvaluator method) KWARG_KEYS (clease.settings.ClusterExpansionSettings attribute)

L

Lasso (class in clease.regression) last_move (clease.datastructures.mc_step.MCStep attribute) LinearRegression (class in clease.regression) load() (clease.basis_function.BasisFunction class method) (clease.datastructures.mc_step.MCStep class method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing static method) (clease.settings.ClusterExpansionSettings class method) (clease.settings.Concentration class method) (clease.settings.concentration.Concentration class method)

load_eci() (clease.evaluate.Evaluate method) load_eci_dict() (clease.evaluate.Evaluate method) log_likelihood_for_each_gamma() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) loocv() (clease.evaluate.Evaluate method) loocv_fast() (clease.evaluate.Evaluate method) lowest_energy (clease.montecarlo.observers.LowestEnergyStructure property) LowestEnergyStructure (class in clease.montecarlo.observers)

M

made_changes() (clease.montecarlo.trial_move_generator.SingleTrialMoveGenerator method) mae() (clease.evaluate.Evaluate method) make_corr_func_data_manager() (in module clease.data_manager) make_valid() (clease.regression.ga_fit.GAFit static method) max_cluster_dia (clease.settings.ClusterExpansionSettings property) max_cluster_size (clease.settings.ClusterExpansionSettings property) max_iter (clease.regression.Lasso property) max_sphere_dia_in_cell() (in module clease.geometry) MaxAttemptReachedError MCConstraint (class in clease.montecarlo.constraints) MCEvaluator (class in clease.montecarlo.mc_evaluator) MCObserver (class in clease.montecarlo.observers) MCStep (class in clease.datastructures.mc_step) meta_info (clease.montecarlo.montecarlo.Montecarlo property) MixedSwapFlip (class in clease.montecarlo.trial_move_generator) module clease.corr_func clease.data_manager clease.geometry clease.montecarlo.constraints clease.montecarlo.observers clease.plot_post_process clease.settings clease.settings.concentration clease.structgen.new_struct clease.tools

Montecarlo (class in clease.montecarlo.montecarlo) move_accepted (clease.datastructures.mc_step.MCStep attribute) move_rejected (clease.datastructures.mc_step.MCStep property) MoveObserver (class in clease.montecarlo.observers) mu() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) multiplicity_factor (clease.settings.ClusterExpansionSettings property) MultiStateSGCConcObserver (class in clease.montecarlo.observers) mutate() (clease.regression.ga_fit.GAFit method)

N

name (clease.basis_function.BasisFunction attribute) (clease.basis_function.BinaryLinear attribute) (clease.basis_function.Polynomial attribute) (clease.basis_function.Trigonometric attribute) (clease.data_manager.FinalStructPropertyGetter property) (clease.montecarlo.constraints.FixedIndices attribute) (clease.montecarlo.constraints.MCConstraint attribute) NAME (clease.montecarlo.montecarlo.Montecarlo attribute) name (clease.montecarlo.observers.ConcentrationObserver attribute) (clease.montecarlo.observers.CorrelationFunctionObserver attribute) (clease.montecarlo.observers.EnergyEvolution attribute) (clease.montecarlo.observers.EnergyPlotUpdater attribute) (clease.montecarlo.observers.LowestEnergyStructure attribute) (clease.montecarlo.observers.MCObserver attribute) (clease.montecarlo.observers.MultiStateSGCConcObserver attribute) (clease.montecarlo.observers.SGCObserver attribute) (clease.montecarlo.observers.SiteOrderParameter attribute) (clease.montecarlo.observers.Snapshot attribute) (clease.montecarlo.trial_move_generator.TrialMoveGenerator property)

name_matches() (clease.montecarlo.trial_move_generator.SingleTrialMoveGenerator method) names (clease.data_manager.CorrelationFunctionGetter property) new_concentration() (clease.montecarlo.observers.ConcentrationObserver method) NewStructures (class in clease.structgen.new_struct) non_background_indices (clease.settings.ClusterExpansionSettings property) num_active_sublattices (clease.settings.ClusterExpansionSettings property) num_basis (clease.settings.ClusterExpansionSettings property) num_cf (clease.settings.ClusterExpansionSettings property) num_data (clease.regression.ga_fit.GAFit property) num_ecis (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing property) num_elements (clease.settings.ClusterExpansionSettings property) num_in_gen() (clease.structgen.new_struct.NewStructures method) num_to_gen() (clease.structgen.new_struct.NewStructures method) num_unique_elements (clease.basis_function.BasisFunction property) (clease.settings.ClusterExpansionSettings property)

O

observe_singlets (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo property) observe_step() (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.LowestEnergyStructure method) (clease.montecarlo.observers.MCObserver method) (clease.montecarlo.observers.MoveObserver method) (clease.montecarlo.observers.SGCObserver method) on_move_accepted() (clease.montecarlo.trial_move_generator.MixedSwapFlip method) (clease.montecarlo.trial_move_generator.RandomSwap method) (clease.montecarlo.trial_move_generator.TrialMoveGenerator method)

on_move_rejected() (clease.montecarlo.trial_move_generator.MixedSwapFlip method) (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) optimal_gamma() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) optimal_inv_variance() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) optimal_lamb() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) optimal_shape_lamb() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) other (clease.datastructures.mc_step.MCStep attribute) OTHER_KEYS (clease.settings.ClusterExpansionSettings attribute)

P

PairConstraint (class in clease.montecarlo.constraints) PhysicalRidge (class in clease.regression.physical_ridge) plot_convex_hull() (in module clease.plot_post_process) plot_CV() (clease.evaluate.Evaluate method) plot_cv() (in module clease.plot_post_process) plot_ECI() (clease.evaluate.Evaluate method) plot_eci() (in module clease.plot_post_process) plot_evolution() (clease.regression.ga_fit.GAFit method) plot_fit() (clease.evaluate.Evaluate method) (in module clease.plot_post_process)

plot_fit_residual() (in module clease.plot_post_process) Polynomial (class in clease.basis_function) population_diversity() (clease.regression.ga_fit.GAFit method) precision_matrix() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) (clease.regression.Lasso method) (clease.regression.LinearRegression method) (clease.regression.Tikhonov method) prefix (clease.montecarlo.observers.SGCState property) prepare_new_active_template() (clease.settings.ClusterExpansionSettings method) prim_cell (clease.settings.ClusterExpansionSettings property) print_coverage_report() (clease.evaluate.Evaluate method)

R

RandomFlip (class in clease.montecarlo.trial_move_generator) RandomFlipWithinBasis (class in clease.montecarlo.trial_move_generator) RandomSwap (class in clease.montecarlo.trial_move_generator) rate (clease.montecarlo.observers.AcceptanceRate property) reconfigure_db_entries() (clease.corr_func.CorrFunction method) reconfigure_inconsistent_cf_table_entries() (clease.corr_func.CorrFunction method) reconfigure_single_db_entry() (clease.corr_func.CorrFunction method) reconstruct() (clease.montecarlo.observers.MoveObserver method) reconstruct_iter() (clease.montecarlo.observers.MoveObserver method) ref_index_trans_symm (clease.settings.ClusterExpansionSettings property) remove_constraints() (clease.montecarlo.trial_move_generator.TrialMoveGenerator method) requires_build() (clease.settings.ClusterExpansionSettings method) reset() (clease.montecarlo.mc_evaluator.MCEvaluator method) (clease.montecarlo.montecarlo.Montecarlo method) (clease.montecarlo.observers.AcceptanceRate method) (clease.montecarlo.observers.ConcentrationObserver method) (clease.montecarlo.observers.CorrelationFunctionObserver method) (clease.montecarlo.observers.DiffractionObserver method) (clease.montecarlo.observers.EnergyEvolution method) (clease.montecarlo.observers.EntropyProductionRate method) (clease.montecarlo.observers.LowestEnergyStructure method) (clease.montecarlo.observers.MCObserver method) (clease.montecarlo.observers.MoveObserver method) (clease.montecarlo.observers.MultiStateSGCConcObserver method) (clease.montecarlo.observers.SGCObserver method) (clease.montecarlo.observers.SGCState method) (clease.montecarlo.observers.SiteOrderParameter method) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method)

reset_averagers() (clease.montecarlo.montecarlo.Montecarlo method) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) reset_eci() (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) rmse() (clease.evaluate.Evaluate method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) run() (clease.montecarlo.montecarlo.Montecarlo method) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) (clease.regression.ga_fit.GAFit method)

S

save() (clease.basis_function.BasisFunction method) (clease.datastructures.mc_step.MCStep method) (clease.montecarlo.observers.EnergyEvolution method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) (clease.settings.ClusterExpansionSettings method) (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) save_eci() (clease.evaluate.Evaluate method) save_population() (clease.regression.ga_fit.GAFit method) scoring_scheme (clease.evaluate.Evaluate property) selected (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing property) SequentialClusterRidge (class in clease.regression.sequential_cluster_ridge) set_active_template() (clease.settings.ClusterExpansionSettings method) set_conc_formula_unit() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) set_conc_ranges() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) set_fitting_scheme() (clease.evaluate.Evaluate method) set_normalization() (clease.evaluate.Evaluate method) set_template() (clease.corr_func.CorrFunction method) settings (clease.corr_func.CorrFunction property) (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo property)

settings_from_json() (in module clease.settings) SGCMonteCarlo (class in clease.montecarlo.sgc_montecarlo) SGCObserver (class in clease.montecarlo.observers) SGCState (class in clease.montecarlo.observers) show_shape_parameter() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) singl_eng (clease.montecarlo.observers.SGCObserver property) singlet2composition() (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method) SingleTrialMoveGenerator (class in clease.montecarlo.trial_move_generator) singlets (clease.montecarlo.observers.SGCObserver property) SiteOrderParameter (class in clease.montecarlo.observers) size (clease.settings.ClusterExpansionSettings property) size_decay (clease.regression.physical_ridge.PhysicalRidge property) sizes_from_names() (clease.regression.physical_ridge.PhysicalRidge method) skew_threshold (clease.settings.ClusterExpansionSettings property) Snapshot (class in clease.montecarlo.observers) spin_dict (clease.basis_function.BasisFunction property) (clease.settings.ClusterExpansionSettings property) step (clease.datastructures.mc_step.MCStep attribute) supercell_factor (clease.settings.ClusterExpansionSettings property) supercell_which_contains_sphere() (in module clease.geometry) support_fast_loocv (clease.regression.Lasso property) (clease.regression.LinearRegression property) synchronize() (clease.montecarlo.mc_evaluator.MCEvaluator method)

T

T (clease.montecarlo.base.BaseMC property) temperature (clease.montecarlo.base.BaseMC property) template_atoms (clease.settings.ClusterExpansionSettings property) Tikhonov (class in clease.regression) to_csv() (clease.data_manager.DataManager method) to_float_conc() (clease.settings.Concentration method) (clease.settings.concentration.Concentration method) todict() (clease.basis_function.BasisFunction method) (clease.basis_function.BinaryLinear method) (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) (clease.settings.ClusterExpansionSettings method) (clease.settings.Concentration method) (clease.settings.concentration.Concentration method)

trans_matrix (clease.settings.ClusterExpansionSettings property) TrialMoveGenerator (class in clease.montecarlo.trial_move_generator) Trigonometric (class in clease.basis_function) trivial_bounds (clease.settings.Concentration property) (clease.settings.concentration.Concentration property)

U

undo_system_changes() (clease.montecarlo.mc_evaluator.MCEvaluator method) unique_element_without_background() (clease.settings.ClusterExpansionSettings method) unique_elements (clease.basis_function.BasisFunction property) (clease.settings.ClusterExpansionSettings property)

update() (clease.montecarlo.observers.EntropyProductionRate method) update_current_energy() (clease.montecarlo.montecarlo.Montecarlo method) update_db() (in module clease.tools) update_quantities() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method) update_sigma_mu() (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method)

V

view_clusters() (clease.settings.ClusterExpansionSettings method)

view_templates() (clease.settings.ClusterExpansionSettings method)

W

weight_matrix (clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing property) (clease.regression.Lasso property) (clease.regression.LinearRegression property)

weights (clease.montecarlo.trial_move_generator.MixedSwapFlip property)