Index

A

add_structure() (icet.StructureContainer method) Advanced topics Cluster counts Cluster vectors Data container Mapping structures Parallel Monte Carlo simulations Special quasirandom structures Structure enumeration Structure mapping analyze_data() (in module mchammer.data_analysis) (mchammer.DataContainer method)

append() (mchammer.DataContainer method) (mchammer.WangLandauDataContainer method) apply_observer() (mchammer.DataContainer method) (mchammer.WangLandauDataContainer method) ARDR assert_structure_compatibility() (icet.ClusterSpace method) attach_observer() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) (mchammer.ensembles.WangLandauEnsemble method) available_properties() (icet.StructureContainer property)

B

Background BCC Bibliography BinaryShortRangeOrderObserver (class in mchammer.observers) boltzmann_constant() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property)

bootstrap() (icet.fitting.EnsembleOptimizer property)

C

calculate_local_contribution() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.calculators.TargetVectorCalculator method) calculate_total() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.calculators.TargetVectorCalculator method) calculator() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) CanonicalAnnealing (class in mchammer.ensembles) CanonicalEnsemble (class in mchammer.ensembles) CE CEs chemical_potentials() (mchammer.ensembles.SemiGrandCanonicalEnsemble property) chemical_symbols() (icet.ClusterSpace property) Class reference BinaryShortRangeOrderObserver CanonicalAnnealing CanonicalEnsemble ClusterCountObserver ClusterExpansion ClusterExpansionCalculator ClusterExpansionObserver ClusterSpace ConfigurationManager Convex hull CrossValidationEstimator DataContainer EnsembleOptimizer Ground state finder HybridEnsemble Optimizer optimizers Other structure tools SemiGrandCanonicalEnsemble SiteOccupancyObserver Special structures SQS generation Structure containers Structure enumeration TargetVectorCalculator Tools User interface; icet User interface; mchammer VCSGCEnsemble WangLandauDataContainer WangLandauEnsemble Wyckoff sites

Cluster Cluster expansion Construction Formalism Cluster size Cluster space cluster_expansion() (mchammer.calculators.ClusterExpansionCalculator property) cluster_space (icet.ClusterExpansion attribute) cluster_space() (icet.StructureContainer property) ClusterCountObserver (class in mchammer.observers) ClusterExpansion (class in icet) ClusterExpansionCalculator (class in mchammer.calculators) ClusterExpansionObserver (class in mchammer.observers) ClusterSpace (class in icet) compare_cluster_vectors() (in module mchammer.calculators) Compressive sensing compute_rmse() (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) concentrations (icet.tools.ConvexHull attribute) ConfigurationManager (class in mchammer) contributions_test() (icet.fitting.Optimizer property) contributions_train() (icet.fitting.Optimizer property) converged() (mchammer.ensembles.WangLandauEnsemble property) ConvexHull (class in icet.tools) copy() (icet.ClusterSpace method) Credits Cross validation CrossValidationEstimator (class in icet.fitting) Crystal symmetry operation Cutoff cutoffs() (icet.ClusterSpace property) CV

D

data() (mchammer.DataContainer property) (mchammer.WangLandauDataContainer property) data_container() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) DataContainer (class in mchammer) DFT dimensions (icet.tools.ConvexHull attribute) do_canonical_swap() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method)

do_sgc_flip() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) do_vcsgc_flip() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) DOS

E

ECI ECIs energies (icet.tools.ConvexHull attribute) ensemble_parameters() (mchammer.DataContainer property) (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) (mchammer.WangLandauDataContainer property)

ensemble_size() (icet.fitting.EnsembleOptimizer property) EnsembleOptimizer (class in icet.fitting) enumerate_structures() (in module icet.tools) enumerate_supercells() (in module icet.tools) error_matrix() (icet.fitting.EnsembleOptimizer property) estimated_ground_state() (mchammer.ensembles.CanonicalAnnealing property) estimated_ground_state_potential() (mchammer.ensembles.CanonicalAnnealing property) evaluate_cluster_function() (icet.ClusterSpace method) Examples Wang-Landau simulations extract_low_energy_structures() (icet.tools.ConvexHull method)

F

FCC fill_factor() (mchammer.ensembles.WangLandauEnsemble property) (mchammer.WangLandauDataContainer property) fill_factor_history() (mchammer.ensembles.WangLandauEnsemble property) (mchammer.WangLandauDataContainer property) fill_factor_limit() (mchammer.ensembles.WangLandauEnsemble property) fit_method() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) flatness_check_interval() (mchammer.ensembles.WangLandauEnsemble property) flatness_limit() (mchammer.ensembles.WangLandauEnsemble property) fractional_position_tolerance() (icet.ClusterExpansion property) (icet.ClusterSpace property) Function reference ClusterExpansion ClusterExpansionCalculator ClusterSpace Convex hull Ground state finder optimizers Other structure tools Special structures SQS generation Structure containers Structure enumeration Structure mapping TargetVectorCalculator Tools User interface; icet User interface; mchammer Wyckoff sites

G

generate_sqs() (in module icet.tools.structure_generation) generate_sqs_by_enumeration() (in module icet.tools.structure_generation) generate_sqs_from_supercells() (in module icet.tools.structure_generation) generate_target_structure() (in module icet.tools.structure_generation) generate_target_structure_from_supercells() (in module icet.tools.structure_generation) get() (mchammer.DataContainer method) (mchammer.WangLandauDataContainer method) get_autocorrelation_function() (in module mchammer.data_analysis) get_average() (mchammer.DataContainer method) get_average_cluster_vectors_wl() (in module mchammer.data_containers) get_average_observables_wl() (in module mchammer.data_containers) get_chemical_symbols() (icet.ClusterSpace method) get_cluster_space_copy() (icet.ClusterExpansion method) get_cluster_vector() (icet.ClusterSpace method) get_condition_number() (icet.StructureContainer method) get_contributions() (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) get_coordinates_of_representative_cluster() (icet.ClusterSpace method) get_correlation_length() (in module mchammer.data_analysis) get_cutoffs() (icet.ClusterSpace method) get_density_of_states_wl() (in module mchammer.data_containers) get_energy_at_convex_hull() (icet.tools.ConvexHull method) get_entropy() (mchammer.ensembles.WangLandauEnsemble method) (mchammer.WangLandauDataContainer method) get_error_estimate() (in module mchammer.data_analysis) get_fit_data() (icet.StructureContainer method) get_flip_state() (mchammer.ConfigurationManager method)

get_ground_state() (icet.tools.ground_state_finder.GroundStateFinder method) get_histogram() (mchammer.ensembles.WangLandauEnsemble method) (mchammer.WangLandauDataContainer method) get_multi_component_vector_permutations() (icet.ClusterSpace method) get_multi_component_vectors_by_orbit() (icet.ClusterSpace method) get_number_of_allowed_species_by_site() (icet.ClusterSpace method) get_number_of_orbits_by_order() (icet.ClusterSpace method) get_observable() (mchammer.observers.BinaryShortRangeOrderObserver method) (mchammer.observers.ClusterCountObserver method) (mchammer.observers.ClusterExpansionObserver method) (mchammer.observers.SiteOccupancyObserver method) get_occupations_on_sublattice() (mchammer.ConfigurationManager method) get_orbit() (icet.ClusterSpace method) get_possible_orbit_occupations() (icet.ClusterSpace method) get_primitive_structure() (in module icet.tools) get_random_sublattice_index() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) (mchammer.ensembles.WangLandauEnsemble method) get_structure_indices() (icet.StructureContainer method) get_sublattices() (icet.ClusterSpace method) get_swapped_state() (mchammer.ConfigurationManager method) get_trajectory() (mchammer.DataContainer method) (mchammer.WangLandauDataContainer method) get_wyckoff_sites() (in module icet.tools) Glossary GroundStateFinder (class in icet.tools.ground_state_finder)

H

HybridEnsemble (class in mchammer.ensembles)

I

icet (module) icet.fitting (module) icet.tools (module) icet.tools.structure_generation (module) Installation

interval (mchammer.observers.BinaryShortRangeOrderObserver attribute) (mchammer.observers.ClusterCountObserver attribute) (mchammer.observers.ClusterExpansionObserver attribute) (mchammer.observers.SiteOccupancyObserver attribute) is_supercell_self_interacting() (icet.ClusterSpace method) is_swap_possible() (mchammer.ConfigurationManager method)

K

kappa() (mchammer.ensembles.VCSGCEnsemble property)

Kernel ridge regression

L

LASSO

M

map_structure_to_reference() (in module icet.tools) MC mchammer.calculators (module) mchammer.data_analysis (module) mchammer.ensembles (module) mchammer.observers (module) MCS MCSs metadata() (icet.ClusterExpansion property) (mchammer.DataContainer property) (mchammer.WangLandauDataContainer property) model() (icet.tools.ground_state_finder.GroundStateFinder property) Monte Carlo Calculators Canonical ensemble, [1] Cluster count observer Cluster expansion calculator Cluster expansion observer Configuration manager Data container data container Ensembles Hybrid ensemble Observers Semi-grand canonical ensemble Short-range order observer Site occupancy observer Target vector calculator Variance-constrained semi-grand canonical ensemble Wang-Landau data container Wang-Landau ensemble

N

n_nonzero_parameters() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) n_nonzero_parameters_splits() (icet.fitting.CrossValidationEstimator property) n_parameters() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property)

n_splits() (icet.fitting.CrossValidationEstimator property) n_steps() (mchammer.ensembles.CanonicalAnnealing property) n_target_values() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property)

O

observables() (mchammer.DataContainer property) (mchammer.WangLandauDataContainer property) observer_interval() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) observers() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property)

occupations() (mchammer.ConfigurationManager property) occupy_structure_randomly() (in module icet.tools.structure_generation) Optimization optimization_status() (icet.tools.ground_state_finder.GroundStateFinder property) Optimizer (class in icet.fitting) Orbit orbit_data() (icet.ClusterSpace property) orbit_list() (icet.ClusterSpace property) Orbits orders() (icet.ClusterExpansion property)

P

parameter_vectors() (icet.fitting.EnsembleOptimizer property) parameters (icet.ClusterExpansion attribute) parameters() (icet.ClusterExpansion property) (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) parameters_as_dataframe() (icet.ClusterExpansion property) parameters_norm() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) parameters_splits() (icet.fitting.CrossValidationEstimator property) parameters_std() (icet.fitting.EnsembleOptimizer property) phis() (mchammer.ensembles.VCSGCEnsemble property) plot_parameters() (icet.ClusterExpansion method)

position_tolerance() (icet.ClusterExpansion property) (icet.ClusterSpace property) predict() (icet.ClusterExpansion method) (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) primitive_structure() (icet.ClusterExpansion property) (icet.ClusterSpace property) print_overview() (icet.ClusterExpansion method) (icet.ClusterSpace method) (icet.StructureContainer method) probabilities() (mchammer.ensembles.HybridEnsemble property) prune() (icet.ClusterExpansion method) Publications

R

random_seed() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) read() (icet.ClusterExpansion static method) (icet.ClusterSpace static method) (icet.StructureContainer static method) (mchammer.DataContainer class method) (mchammer.WangLandauDataContainer class method) Regularization return_type() (mchammer.observers.BinaryShortRangeOrderObserver property) (mchammer.observers.ClusterCountObserver property) (mchammer.observers.ClusterExpansionObserver property) (mchammer.observers.SiteOccupancyObserver property) RFE

rmse_test() (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) rmse_test_ensemble() (icet.fitting.EnsembleOptimizer property) rmse_train() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) rmse_train_ensemble() (icet.fitting.EnsembleOptimizer property) rmse_train_final() (icet.fitting.CrossValidationEstimator property) rmse_train_splits() (icet.fitting.CrossValidationEstimator property) rmse_validation() (icet.fitting.CrossValidationEstimator property) rmse_validation_splits() (icet.fitting.CrossValidationEstimator property) run() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) (mchammer.ensembles.WangLandauEnsemble method)

S

seed() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) SemiGrandCanonicalEnsemble (class in mchammer.ensembles) SiteOccupancyObserver (class in mchammer.observers) space_group() (icet.ClusterSpace property) species_maps() (icet.ClusterSpace property) standardize() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) step() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) structure() (mchammer.calculators.ClusterExpansionCalculator property) (mchammer.calculators.TargetVectorCalculator property) (mchammer.ConfigurationManager property) (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property)

StructureContainer (class in icet) structures (icet.tools.ConvexHull attribute) sublattices() (mchammer.calculators.ClusterExpansionCalculator property) (mchammer.calculators.TargetVectorCalculator property) (mchammer.ConfigurationManager property) (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property) summary() (icet.fitting.CrossValidationEstimator property) (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) symprec() (icet.ClusterExpansion property) (icet.ClusterSpace property)

T

T_start() (mchammer.ensembles.CanonicalAnnealing property) T_stop() (mchammer.ensembles.CanonicalAnnealing property) tag (mchammer.observers.BinaryShortRangeOrderObserver attribute) (mchammer.observers.ClusterCountObserver attribute) (mchammer.observers.ClusterExpansionObserver attribute) (mchammer.observers.SiteOccupancyObserver attribute) TargetVectorCalculator (class in mchammer.calculators) temperature() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) test_fraction() (icet.fitting.Optimizer property) test_scatter_data (icet.fitting.Optimizer attribute) test_set() (icet.fitting.Optimizer property) test_size() (icet.fitting.Optimizer property) train() (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method)

train_fraction() (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) train_scatter_data (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.Optimizer attribute) train_set() (icet.fitting.Optimizer property) train_size() (icet.fitting.EnsembleOptimizer property) (icet.fitting.Optimizer property) trial_steps_per_ensemble() (mchammer.ensembles.HybridEnsemble property) Tutorial Analyze ECIs Analyzing Monte Carlo simulations Compare with target data Constructing a cluster expansion Enumerate structures Monte Carlo simulations

U

update_occupations() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.calculators.TargetVectorCalculator method) (mchammer.ConfigurationManager method) (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) (mchammer.ensembles.WangLandauEnsemble method)

user_tag() (mchammer.ensembles.CanonicalAnnealing property) (mchammer.ensembles.CanonicalEnsemble property) (mchammer.ensembles.HybridEnsemble property) (mchammer.ensembles.SemiGrandCanonicalEnsemble property) (mchammer.ensembles.VCSGCEnsemble property) (mchammer.ensembles.WangLandauEnsemble property)

V

validate() (icet.fitting.CrossValidationEstimator method) validation_method() (icet.fitting.CrossValidationEstimator property)

validation_scatter_data (icet.fitting.CrossValidationEstimator attribute) VCSGCEnsemble (class in mchammer.ensembles)

W

WangLandauDataContainer (class in mchammer) WangLandauEnsemble (class in mchammer.ensembles) WL Workflow write() (icet.ClusterExpansion method) (icet.ClusterSpace method) (icet.StructureContainer method) (mchammer.DataContainer method) (mchammer.WangLandauDataContainer method)

write_data_container() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) (mchammer.ensembles.WangLandauEnsemble method) write_summary() (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method)