CLEASE
Contents:
Release notes
Au-Cu alloy example
Metadynamics sampling
CLEASE Command Line Interface
Importing Structures
API Documentation
Parallelization
Benchmarking
Publications Using CLEASE
Partners and Support
CLEASE
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Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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)
alpha_CV() (clease.evaluate.Evaluate method)
apply_system_changes() (clease.montecarlo.mc_evaluator.MCEvaluator method)
atomic_concentration_ratio (clease.settings.ClusterExpansionSettings property)
atomic_concentrations (clease.evaluate.Evaluate property)
atoms (clease.montecarlo.base.BaseMC 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_functions (clease.basis_function.BasisFunction property)
BasisFunction (class in clease.basis_function)
BayesianCompressiveSensing (class in clease.regression.bayesian_compressive_sensing)
BinaryLinear (class in clease.basis_function)
build() (clease.data_manager.CorrelationFunctionGetterVolDepECI method)
C
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)
cf_table_name (clease.corr_func.CorrFunction property)
check_consistency_of_cf_table_entries() (clease.corr_func.CorrFunction method)
check_valid() (clease.regression.ga_fit.GAFit method)
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
close() (clease.montecarlo.observers.Snapshot method)
cluster_list (clease.settings.ClusterExpansionSettings property)
ClusterExpansionSettings (class in clease.settings)
clusters_table() (clease.settings.ClusterExpansionSettings method)
CollectiveVariableConstraint (class in clease.montecarlo.constraints)
Concentration (class in clease.settings.concentration)
ConcentrationObserver (class in clease.montecarlo.observers)
concentrations (clease.evaluate.Evaluate property)
connect() (clease.settings.ClusterExpansionSettings method)
(clease.structgen.new_struct.NewStructures method)
ConstrainElementInserts (class in clease.montecarlo.constraints)
ConstrainSwapByBasis (class in clease.montecarlo.constraints)
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)
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)
D
DataManager (class in clease.data_manager)
db_name (clease.settings.ClusterExpansionSettings property)
design_matrix() (clease.regression.ga_fit.GAFit method)
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.montecarlo.observers.LowestEnergyStructure 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)
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_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)
from_dict() (clease.settings.ClusterExpansionSettings 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)
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_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_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_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
ignored_species_and_conc (clease.settings.ClusterExpansionSettings property)
InconsistentDataError
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_tracked() (clease.montecarlo.trial_move_generator.RandomSwap 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)
L
Lasso (class in clease.regression)
LinearRegression (class in clease.regression)
load() (clease.basis_function.BasisFunction class method)
(clease.datastructures.mc_step.MCStep class method)
(clease.settings.ClusterExpansionSettings 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)
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_sphere_dia_in_cell() (in module clease.geometry)
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)
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.data_manager.FinalStructPropertyGetter 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_cf (clease.settings.ClusterExpansionSettings property)
O
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)
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.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)
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.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)
save_eci() (clease.evaluate.Evaluate method)
SequentialClusterRidge (class in clease.regression.sequential_cluster_ridge)
set_active_template() (clease.settings.ClusterExpansionSettings method)
set_conc_formula_unit() (clease.settings.concentration.Concentration method)
set_conc_ranges() (clease.settings.concentration.Concentration method)
set_normalization() (clease.evaluate.Evaluate method)
set_template() (clease.corr_func.CorrFunction method)
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)
singlet2composition() (clease.montecarlo.sgc_montecarlo.SGCMonteCarlo method)
SingleTrialMoveGenerator (class in clease.montecarlo.trial_move_generator)
SiteOrderParameter (class in clease.montecarlo.observers)
sizes_from_names() (clease.regression.physical_ridge.PhysicalRidge method)
Snapshot (class in clease.montecarlo.observers)
supercell_which_contains_sphere() (in module clease.geometry)
synchronize() (clease.montecarlo.mc_evaluator.MCEvaluator method)
T
T (clease.montecarlo.base.BaseMC property)
temperature (clease.montecarlo.base.BaseMC property)
Tikhonov (class in clease.regression)
to_csv() (clease.data_manager.DataManager method)
todict() (clease.basis_function.BasisFunction method)
(clease.basis_function.BinaryLinear method)
(clease.regression.bayesian_compressive_sensing.BayesianCompressiveSensing method)
(clease.settings.ClusterExpansionSettings method)
trans_matrix (clease.settings.ClusterExpansionSettings property)
TrialMoveGenerator (class in clease.montecarlo.trial_move_generator)
Trigonometric (class in clease.basis_function)
U
undo_system_changes() (clease.montecarlo.mc_evaluator.MCEvaluator method)
unique_element_without_background() (clease.settings.ClusterExpansionSettings method)
update() (clease.montecarlo.observers.EntropyProductionRate 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
weights (clease.montecarlo.trial_move_generator.MixedSwapFlip property)
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