Index

A

active_structure() (kmcpy.structure.active_site_order.ActiveSiteOrder method) ActiveSiteOrder (class in kmcpy.structure.active_site_order) add() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) add_event() (kmcpy.event.base.EventLib method) add_exact_rule() (kmcpy.models.local_barrier_model.LocalBarrierModel method) add_note() (kmcpy.simulator.tracker.CallbackExecutionError method) add_pattern_rule() (kmcpy.models.local_barrier_model.LocalBarrierModel method) add_rule() (kmcpy.models.local_barrier_model.LocalBarrierModel method) add_species_count_rule() (kmcpy.models.local_barrier_model.LocalBarrierModel method) add_state_count_rule() (kmcpy.models.local_barrier_model.LocalBarrierModel method) add_structure() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) add_structures() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) annotate_event() (kmcpy.event.hop.HopStateLookup method) annotate_event_lib() (kmcpy.event.hop.HopStateLookup method) append() (kmcpy.models.parameters.LCEModelParamHistory method) append_record() (in module kmcpy.simulator.property) apply_event() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.state.State method) apply_property_plan() (kmcpy.simulator.tracker.Tracker method) are_equal() (kmcpy.structure.comparator.SupercellComparator method) array_equal() (kmcpy.structure.basis.Occupation method) as_dict() (kmcpy.event.base.EventLib method) (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.fitting.fitter.BaseFitter method) (kmcpy.models.fitting.fitter.LCEFitter method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.parameters.LCEModelParameters method) (kmcpy.models.parameters.LCEModelParamHistory method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.config.Configuration method) (kmcpy.simulator.config.RuntimeConfig method) (kmcpy.simulator.config.SystemConfig method) (kmcpy.simulator.state.State method) (kmcpy.structure.active_site_order.ActiveSiteOrder method) (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) (kmcpy.structure.cluster.Cluster method) (kmcpy.structure.cluster.Orbit method) (kmcpy.structure.comparator.SupercellComparator method) (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) (kmcpy.structure.local_site_order.LocalSiteOrder method)

as_flip() (kmcpy.models.site_energy.MappedOccupationChange method) as_input_dict() (kmcpy.simulator.config.Configuration method) as_record_dict() (kmcpy.simulator.config.Configuration method) as_system_change_tuple() (kmcpy.models.site_energy.MappedOccupationChange method) assert_same_order() (kmcpy.structure.active_site_order.ActiveSiteOrder method) attach() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method) attach_spec() (kmcpy.simulator.tracker.Tracker method) attempt_frequency (kmcpy.simulator.config.Configuration property)

B

BaseFitter (class in kmcpy.models.fitting.fitter) BaseModel (class in kmcpy.models.base) basis (kmcpy.structure.basis.Occupation property) basis_function (kmcpy.structure.basis.BasisFunction property) (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) basis_obj (kmcpy.structure.basis.Occupation property) BasisFunction (class in kmcpy.structure.basis) build() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method)

build_orbits() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) build_parser() (in module kmcpy.cli.init) (in module kmcpy.cli.main) build_site_index() (in module kmcpy.structure.sites) build_template() (in module kmcpy.cli.init) builtin_enabled (kmcpy.simulator.property.PropertyPlan property) builtin_property_enabled (kmcpy.simulator.config.Configuration property)

C

CallbackExecutionError ChebyshevBasis (class in kmcpy.structure.basis) clear_attachments() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method) clear_event_dependencies() (kmcpy.event.base.EventLib method) Cluster (class in kmcpy.structure.cluster) cluster_site_indices (kmcpy.structure.cluster.Orbit property) ClusterMatch (class in kmcpy.structure.cluster) ClusterMatcher (class in kmcpy.structure.cluster) CompositeLCEModel (class in kmcpy.models.composite_lce_model) compute() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method) compute_occ_corr() (kmcpy.io.neb.data.NEBEntry method) (kmcpy.io.neb.NEBEntry method) compute_probability() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method)

compute_transport_properties() (in module kmcpy.simulator.property) Configuration (class in kmcpy.simulator.config) constant_barrier() (kmcpy.models.local_barrier_model.LocalBarrierModel class method) constant_site_energy_difference() (in module kmcpy.models.site_energy) convert_to() (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) convert_to_primitive_cell (kmcpy.simulator.config.Configuration property) copy() (kmcpy.simulator.state.State method) (kmcpy.structure.basis.Occupation method) (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) correlation (kmcpy.io.neb.data.NEBEntry attribute) (kmcpy.io.neb.NEBEntry attribute) count_match() (kmcpy.structure.basis.Occupation method) count_mismatch() (kmcpy.structure.basis.Occupation method) count_occupied() (kmcpy.structure.basis.Occupation method) count_vacant() (kmcpy.structure.basis.Occupation method)

D

data (kmcpy.structure.basis.Occupation property) describe_property_calculations() (in module kmcpy.simulator.property) detach() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method)

dimension (kmcpy.simulator.config.Configuration property) (kmcpy.simulator.tracker.Tracker property)

E

elem_hop_distance (kmcpy.simulator.tracker.Tracker property) elementary_hop_distance (kmcpy.simulator.config.Configuration property) endpoint_direction_from_codes() (in module kmcpy.event.hop) entry_from_event_state() (kmcpy.models.local_barrier_model.LocalBarrierModel class method) enumerate_local_environments() (in module kmcpy.structure.local_environment_enumerator) enumerate_neb_endpoint_pairs() (in module kmcpy.structure.local_environment_enumerator) equilibration_passes (kmcpy.simulator.config.Configuration property) equivalent_to() (kmcpy.structure.basis.Occupation method)

Event (class in kmcpy.event.base) event_dependencies (kmcpy.event.base.EventLib attribute) event_direction() (in module kmcpy.event.hop) event_file (kmcpy.simulator.config.Configuration property) EventGenerator (class in kmcpy.event.generators) EventLib (class in kmcpy.event.base) events (kmcpy.event.base.EventLib attribute) external_site_order_hash (kmcpy.models.site_energy.SiteEnergyModel property)

F

field_units() (kmcpy.simulator.config.Configuration class method) filter_active_structure() (kmcpy.structure.active_site_order.ActiveSiteOrder method) find_atom_indices() (in module kmcpy.event.generators) find_site_by_wyckoff_sequence_and_label() (in module kmcpy.structure.sites) find_site_by_wyckoff_sequence_label_and_supercell() (in module kmcpy.structure.sites) fingerprint (kmcpy.structure.cluster.Cluster property) (kmcpy.structure.cluster.Orbit property) fit() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.fitting.fitter.BaseFitter method) (kmcpy.models.fitting.fitter.LCEFitter method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method) flip() (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.Occupation method) (kmcpy.structure.basis.OccupationBasis method) flip_inplace() (kmcpy.structure.basis.Occupation method) format_tracker_summary() (in module kmcpy.simulator.results) frac_coords (kmcpy.simulator.tracker.Tracker property) fresh_attachment_specs() (kmcpy.simulator.property.PropertyPlan method) from_active_site_order() (kmcpy.event.hop.HopStateLookup class method) from_chebyshev() (kmcpy.structure.basis.OccupationBasis method) from_config() (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.kmc.KMC class method) from_dict() (kmcpy.event.base.Event class method) (kmcpy.event.base.EventLib class method) (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.fitting.fitter.BaseFitter class method) (kmcpy.models.fitting.fitter.LCEFitter class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.parameters.LCEModelParameters class method) (kmcpy.models.parameters.LCEModelParamHistory class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.config.Configuration class method) (kmcpy.simulator.state.State class method) (kmcpy.structure.active_site_order.ActiveSiteOrder class method) (kmcpy.structure.basis.BasisFunction class method) (kmcpy.structure.basis.ChebyshevBasis class method) (kmcpy.structure.basis.OccupationBasis class method) (kmcpy.structure.cluster.Cluster class method) (kmcpy.structure.cluster.Orbit class method) (kmcpy.structure.comparator.SupercellComparator class method) (kmcpy.structure.local_site_order.LocalSiteOrder class method)

from_exact_entries() (kmcpy.models.local_barrier_model.LocalBarrierModel class method) from_file() (kmcpy.event.base.EventLib class method) (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.parameters.LCEModelParameters class method) (kmcpy.models.parameters.LCEModelParamHistory class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.config.Configuration class method) (kmcpy.simulator.state.State class method) from_lattice_structure() (kmcpy.structure.active_site_order.ActiveSiteOrder class method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure class method) from_name() (kmcpy.structure.local_site_order.LocalSiteOrder class method) from_neighbor_info() (kmcpy.structure.cluster.Cluster class method) from_occupation() (kmcpy.structure.basis.ChebyshevBasis method) from_occupations() (kmcpy.simulator.state.State class method) from_sites() (kmcpy.structure.cluster.Cluster class method) from_structure() (kmcpy.io.neb.data.NEBEntry class method) (kmcpy.io.neb.NEBEntry class method) from_structure_and_mapping() (kmcpy.structure.active_site_order.ActiveSiteOrder class method) from_structures() (kmcpy.io.neb.data.NEBDataLoader class method) (kmcpy.io.neb.NEBDataLoader class method) full_structure_with_properties() (kmcpy.structure.active_site_order.ActiveSiteOrder method)

G

generate_event_dependencies() (kmcpy.event.base.EventLib method) generate_events() (kmcpy.event.generators.EventGenerator method) generate_neb_endpoint_pair() (in module kmcpy.structure.local_environment_enumerator) get_active_lattice_structure() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_active_site_order() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_basis() (in module kmcpy.structure.basis) get_bond_distances() (kmcpy.structure.cluster.Cluster method) get_cluster_function() (kmcpy.structure.cluster.Cluster method) (kmcpy.structure.cluster.Orbit method) get_corr_from_structure() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) get_correlation_matrix() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) get_cutoff_neighbor_info() (in module kmcpy.structure.neighbors) get_dependency_statistics() (kmcpy.event.base.EventLib method) get_dependent_events() (kmcpy.event.base.EventLib method) get_environment_signature() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_event_dependencies_info() (kmcpy.event.base.EventLib method) get_events_involving_site() (kmcpy.event.base.EventLib method) get_fitter_class() (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.site_energy.SiteEnergyModel class method)

get_fitter_for_model() (in module kmcpy.models.fitting.registry) get_hash() (kmcpy.structure.comparator.SupercellComparator method) get_match_indices() (kmcpy.structure.basis.Occupation method) get_mismatch_indices() (kmcpy.structure.basis.Occupation method) get_occ_corr_from_structure() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) get_occ_from_structure() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_occupation_matrix() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) get_occupied_indices() (kmcpy.structure.basis.Occupation method) get_orbit_fingerprints() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) get_ordered_site_hash() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_ordered_site_signature() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_properties() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) get_property_records() (kmcpy.simulator.tracker.Tracker method) get_range_cutoff_neighbor_info() (in module kmcpy.structure.neighbors) get_structure_from_occ() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) get_vacant_indices() (kmcpy.structure.basis.Occupation method) global_interval (kmcpy.simulator.property.PropertyPlan property) global_time_interval (kmcpy.simulator.property.PropertyPlan property)

H

has_event_dependencies() (kmcpy.event.base.EventLib method)

help_fields() (kmcpy.simulator.config.Configuration class method) HopStateLookup (class in kmcpy.event.hop)

I

initial_occupations (kmcpy.simulator.config.Configuration property) initial_state_file (kmcpy.simulator.config.Configuration property) initialize_state() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.site_energy.SiteEnergyModel method)

is_equivalent_to() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) is_occupied() (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) is_vacancy_species() (in module kmcpy.structure.species) is_vacant() (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method)

K

KMC (class in kmcpy.simulator.kmc) kmc_info_key() (in module kmcpy.structure.sites) kmc_passes (kmcpy.simulator.config.Configuration property) kmcpy.api module kmcpy.cli.init module kmcpy.cli.main module kmcpy.cli.run_kmc module kmcpy.event.base module kmcpy.event.generators module kmcpy.event.hop module kmcpy.io.cif module kmcpy.io.neb module kmcpy.io.neb.data module kmcpy.io.registry module kmcpy.models.base module kmcpy.models.composite_lce_model module kmcpy.models.fitting.fitter module kmcpy.models.fitting.registry module kmcpy.models.local_barrier_model module kmcpy.models.local_cluster_expansion module kmcpy.models.parameters module

kmcpy.models.site_energy module kmcpy.simulator.config module kmcpy.simulator.kmc module kmcpy.simulator.property module kmcpy.simulator.results module kmcpy.simulator.state module kmcpy.simulator.tracker module kmcpy.structure.active_site_order module kmcpy.structure.basis module kmcpy.structure.cluster module kmcpy.structure.comparator module kmcpy.structure.lattice_structure module kmcpy.structure.local_environment_enumerator module kmcpy.structure.local_lattice_structure module kmcpy.structure.local_site_order module kmcpy.structure.neighbors module kmcpy.structure.sites module kmcpy.structure.species module kmcpy.units module

L

labels (kmcpy.structure.cluster.Cluster property) latt (kmcpy.simulator.tracker.Tracker property) LatticeStructure (class in kmcpy.structure.lattice_structure) LCEFitter (class in kmcpy.models.fitting.fitter) LCEModelParameters (class in kmcpy.models.parameters) LCEModelParamHistory (class in kmcpy.models.parameters) list_attachments() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method) list_property_calculations() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method) load() (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.fitting.fitter.BaseFitter class method) (kmcpy.models.fitting.fitter.LCEFitter class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.parameters.LCEModelParameters class method) (kmcpy.models.parameters.LCEModelParamHistory class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.config.Configuration class method) (kmcpy.simulator.state.State class method) (kmcpy.structure.active_site_order.ActiveSiteOrder class method) (kmcpy.structure.basis.BasisFunction class method) (kmcpy.structure.basis.ChebyshevBasis class method) (kmcpy.structure.basis.OccupationBasis class method) (kmcpy.structure.cluster.Cluster class method) (kmcpy.structure.cluster.Orbit class method) (kmcpy.structure.comparator.SupercellComparator class method) (kmcpy.structure.local_site_order.LocalSiteOrder class method)

load_checkpoint() (kmcpy.simulator.state.State class method) load_labeled_structure_from_cif() (in module kmcpy.io.cif) load_labeled_structure_from_string() (in module kmcpy.io.cif) load_labeled_structures_from_cif() (in module kmcpy.io.cif) load_parameters_from_file() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) local_env_indices (kmcpy.event.base.Event attribute) LocalBarrierModel (class in kmcpy.models.local_barrier_model) LocalClusterExpansion (class in kmcpy.models.local_cluster_expansion) LocalEnvironmentEnumeration (class in kmcpy.structure.local_environment_enumerator) LocalLatticeStructure (class in kmcpy.structure.local_lattice_structure) LocalSiteOrder (class in kmcpy.structure.local_site_order)

M

main() (in module kmcpy.cli.init) (in module kmcpy.cli.main) (in module kmcpy.cli.run_kmc) make_kmc_supercell() (in module kmcpy.structure.sites) make_property_spec() (in module kmcpy.simulator.property) make_supercell() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) MappedOccupationChange (class in kmcpy.models.site_energy) match() (kmcpy.structure.cluster.ClusterMatcher method) match_clusters() (in module kmcpy.structure.cluster) match_value (kmcpy.structure.basis.BasisFunction property) (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) match_with_reference() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) metadata (kmcpy.io.neb.data.NEBEntry attribute) (kmcpy.io.neb.NEBEntry attribute) mismatch_value (kmcpy.structure.basis.BasisFunction property) (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) mobile_ion_charge (kmcpy.simulator.config.Configuration property) mobile_ion_indices (kmcpy.event.base.Event attribute) mobile_ion_specie (kmcpy.simulator.config.Configuration property) (kmcpy.simulator.tracker.Tracker property) model_file (kmcpy.simulator.config.Configuration property) model_name (kmcpy.io.neb.data.NEBDataLoader attribute) (kmcpy.io.neb.NEBDataLoader attribute) model_type (kmcpy.simulator.config.Configuration property) module kmcpy.api kmcpy.cli.init kmcpy.cli.main kmcpy.cli.run_kmc kmcpy.event.base kmcpy.event.generators kmcpy.event.hop kmcpy.io.cif kmcpy.io.neb kmcpy.io.neb.data kmcpy.io.registry kmcpy.models.base kmcpy.models.composite_lce_model kmcpy.models.fitting.fitter kmcpy.models.fitting.registry kmcpy.models.local_barrier_model kmcpy.models.local_cluster_expansion kmcpy.models.parameters kmcpy.models.site_energy kmcpy.simulator.config kmcpy.simulator.kmc kmcpy.simulator.property kmcpy.simulator.results kmcpy.simulator.state kmcpy.simulator.tracker kmcpy.structure.active_site_order kmcpy.structure.basis kmcpy.structure.cluster kmcpy.structure.comparator kmcpy.structure.lattice_structure kmcpy.structure.local_environment_enumerator kmcpy.structure.local_lattice_structure kmcpy.structure.local_site_order kmcpy.structure.neighbors kmcpy.structure.sites kmcpy.structure.species kmcpy.units

N

name (kmcpy.models.base.BaseModel attribute) (kmcpy.simulator.config.Configuration property) NEBDataLoader (class in kmcpy.io.neb) (class in kmcpy.io.neb.data) NEBEndpointPair (class in kmcpy.structure.local_environment_enumerator) NEBEntry (class in kmcpy.io.neb) (class in kmcpy.io.neb.data)

normalize_species() (in module kmcpy.structure.species) normalize_supercell_tuple() (in module kmcpy.event.generators) num_site_basis_functions() (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method)

O

occ_initial (kmcpy.simulator.tracker.Tracker property) Occupation (class in kmcpy.structure.basis) occupation (kmcpy.io.neb.data.NEBEntry attribute) (kmcpy.io.neb.NEBEntry attribute) occupation_value_for_species() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) OccupationBasis (class in kmcpy.structure.basis)

occupied_value (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) ones() (kmcpy.structure.basis.Occupation class method) Orbit (class in kmcpy.structure.cluster) ordered_candidate_indices() (kmcpy.structure.cluster.ClusterMatcher method) ordered_neighbor_info_from_finder() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure class method) ordered_site_hash() (in module kmcpy.structure.local_site_order) ordered_site_signature() (in module kmcpy.structure.local_site_order)

P

point_group_symbol (kmcpy.structure.cluster.Cluster property) prepare_cutoff_neighbor_lookup() (in module kmcpy.structure.neighbors) prepare_range_cutoff_neighbor_lookup() (in module kmcpy.structure.neighbors) prepare_range_cutoff_neighbor_lookup_from_preset() (in module kmcpy.structure.neighbors) property_callbacks (kmcpy.simulator.config.Configuration property) property_sampling_interval (kmcpy.simulator.config.Configuration property)

property_sampling_time_interval (kmcpy.simulator.config.Configuration property) property_value (kmcpy.io.neb.data.NEBEntry attribute) (kmcpy.io.neb.NEBEntry attribute) PropertyPlan (class in kmcpy.simulator.property) PropertyRecord (class in kmcpy.simulator.property) PropertySpec (class in kmcpy.simulator.property) propose() (kmcpy.simulator.kmc.KMC method)

Q

q (kmcpy.simulator.tracker.Tracker property)

R

random() (kmcpy.structure.basis.Occupation class method) random_seed (kmcpy.simulator.config.Configuration property) register_basis() (in module kmcpy.structure.basis) register_fitter() (in module kmcpy.models.fitting.registry) require_model_file_payload() (in module kmcpy.models.base) require_model_type() (in module kmcpy.models.base) resolve() (kmcpy.structure.local_site_order.LocalSiteOrder class method)

resolve_callable_reference() (in module kmcpy.models.site_energy) result_units (kmcpy.simulator.tracker.Tracker property) return_current_info() (kmcpy.simulator.tracker.Tracker method) run() (in module kmcpy.api) (kmcpy.simulator.kmc.KMC method) run_kmc() (in module kmcpy.cli.run_kmc) RuntimeConfig (class in kmcpy.simulator.config)

S

sample_properties() (kmcpy.simulator.tracker.Tracker method) save() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.fitting.fitter.BaseFitter method) (kmcpy.models.fitting.fitter.LCEFitter method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.parameters.LCEModelParameters method) (kmcpy.models.parameters.LCEModelParamHistory method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.config.Configuration method) (kmcpy.simulator.state.State method) (kmcpy.structure.active_site_order.ActiveSiteOrder method) (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) (kmcpy.structure.cluster.Cluster method) (kmcpy.structure.cluster.Orbit method) (kmcpy.structure.comparator.SupercellComparator method) (kmcpy.structure.local_site_order.LocalSiteOrder method) save_checkpoint() (kmcpy.simulator.state.State method) select_active_values() (kmcpy.structure.active_site_order.ActiveSiteOrder method) set_frequency() (kmcpy.simulator.property.PropertyPlan method) set_global_property_frequency() (kmcpy.simulator.tracker.Tracker method) set_index_metadata() (kmcpy.event.base.EventLib method) set_parameters() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) set_property_enabled() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.property.PropertyPlan method) (kmcpy.simulator.tracker.Tracker method) set_property_enabled_flag() (in module kmcpy.simulator.property)

set_property_frequency() (kmcpy.simulator.kmc.KMC method) should_trigger() (in module kmcpy.simulator.property) show_current_info() (kmcpy.simulator.tracker.Tracker method) show_info() (kmcpy.event.base.Event method) show_project_info() (kmcpy.simulator.kmc.KMC method) signature (kmcpy.structure.cluster.Cluster property) site_basis_values() (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) site_index_key() (in module kmcpy.structure.sites) site_mapping (kmcpy.simulator.config.Configuration property) site_to_events (kmcpy.event.base.EventLib attribute) SiteEnergyModel (class in kmcpy.models.site_energy) sort_local_env_sites() (kmcpy.structure.local_site_order.LocalSiteOrder method) sort_neighbor_info() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure static method) species_equivalent() (in module kmcpy.structure.species) species_for_occupation_value() (kmcpy.structure.lattice_structure.LatticeStructure method) (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) species_label() (in module kmcpy.structure.species) species_tokens() (in module kmcpy.structure.species) State (class in kmcpy.simulator.state) state_value() (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) structure_file (kmcpy.simulator.config.Configuration property) structure_from_sites() (in module kmcpy.structure.sites) summary() (kmcpy.simulator.config.Configuration method) supercell_shape (kmcpy.simulator.config.Configuration property) SupercellComparator (class in kmcpy.structure.comparator) SystemConfig (class in kmcpy.simulator.config)

T

temperature (kmcpy.simulator.config.Configuration property) (kmcpy.simulator.tracker.Tracker property) time (kmcpy.simulator.tracker.Tracker property) to() (kmcpy.event.base.EventLib method) (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.parameters.LCEModelParameters method) (kmcpy.models.parameters.LCEModelParamHistory method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.config.Configuration method) to_basis() (kmcpy.structure.basis.Occupation method) to_chebyshev() (kmcpy.structure.basis.OccupationBasis method) to_cluster() (kmcpy.structure.local_lattice_structure.LocalLatticeStructure method) to_json() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.fitting.fitter.BaseFitter method) (kmcpy.models.fitting.fitter.LCEFitter method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.parameters.LCEModelParameters method) (kmcpy.models.parameters.LCEModelParamHistory method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.config.Configuration method) (kmcpy.simulator.state.State method) (kmcpy.structure.active_site_order.ActiveSiteOrder method) (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) (kmcpy.structure.cluster.Cluster method) (kmcpy.structure.cluster.Orbit method) (kmcpy.structure.comparator.SupercellComparator method) (kmcpy.structure.local_site_order.LocalSiteOrder method)

to_occupation() (kmcpy.structure.basis.ChebyshevBasis method) to_xyz() (kmcpy.structure.cluster.Cluster method) Tracker (class in kmcpy.simulator.tracker)

U

unit_factor_to_mev (kmcpy.models.site_energy.SiteEnergyModel property) unit_for() (in module kmcpy.units) unsafe_hash() (kmcpy.models.base.BaseModel method) (kmcpy.models.composite_lce_model.CompositeLCEModel method) (kmcpy.models.fitting.fitter.BaseFitter method) (kmcpy.models.fitting.fitter.LCEFitter method) (kmcpy.models.local_barrier_model.LocalBarrierModel method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) (kmcpy.models.parameters.LCEModelParameters method) (kmcpy.models.parameters.LCEModelParamHistory method) (kmcpy.models.site_energy.SiteEnergyModel method) (kmcpy.simulator.config.Configuration method) (kmcpy.simulator.state.State method) (kmcpy.structure.active_site_order.ActiveSiteOrder method) (kmcpy.structure.basis.BasisFunction method) (kmcpy.structure.basis.ChebyshevBasis method) (kmcpy.structure.basis.OccupationBasis method) (kmcpy.structure.cluster.Cluster method) (kmcpy.structure.cluster.Orbit method) (kmcpy.structure.comparator.SupercellComparator method) (kmcpy.structure.local_site_order.LocalSiteOrder method)

update() (kmcpy.simulator.kmc.KMC method) (kmcpy.simulator.tracker.Tracker method) update_current_pass() (kmcpy.simulator.tracker.Tracker method) uses_state_indices (kmcpy.structure.basis.BasisFunction property) (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property)

V

v (kmcpy.simulator.tracker.Tracker property) vacancy_species() (in module kmcpy.structure.species) vacant_value (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) valid_values (kmcpy.structure.basis.BasisFunction property) (kmcpy.structure.basis.ChebyshevBasis property) (kmcpy.structure.basis.OccupationBasis property) validate() (kmcpy.simulator.config.Configuration method) validate_active_indices() (kmcpy.structure.active_site_order.ActiveSiteOrder method) validate_index_metadata() (kmcpy.event.base.EventLib method) validate_max_records() (in module kmcpy.simulator.property) validate_monty_v1() (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.fitting.fitter.BaseFitter class method) (kmcpy.models.fitting.fitter.LCEFitter class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.parameters.LCEModelParameters class method) (kmcpy.models.parameters.LCEModelParamHistory class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.config.Configuration class method) (kmcpy.simulator.state.State class method) (kmcpy.structure.active_site_order.ActiveSiteOrder class method) (kmcpy.structure.basis.BasisFunction class method) (kmcpy.structure.basis.ChebyshevBasis class method) (kmcpy.structure.basis.OccupationBasis class method) (kmcpy.structure.cluster.Cluster class method) (kmcpy.structure.cluster.Orbit class method) (kmcpy.structure.comparator.SupercellComparator class method) (kmcpy.structure.local_site_order.LocalSiteOrder class method)

validate_monty_v2() (kmcpy.models.base.BaseModel class method) (kmcpy.models.composite_lce_model.CompositeLCEModel class method) (kmcpy.models.fitting.fitter.BaseFitter class method) (kmcpy.models.fitting.fitter.LCEFitter class method) (kmcpy.models.local_barrier_model.LocalBarrierModel class method) (kmcpy.models.local_cluster_expansion.LocalClusterExpansion class method) (kmcpy.models.parameters.LCEModelParameters class method) (kmcpy.models.parameters.LCEModelParamHistory class method) (kmcpy.models.site_energy.SiteEnergyModel class method) (kmcpy.simulator.config.Configuration class method) (kmcpy.simulator.state.State class method) (kmcpy.structure.active_site_order.ActiveSiteOrder class method) (kmcpy.structure.basis.BasisFunction class method) (kmcpy.structure.basis.ChebyshevBasis class method) (kmcpy.structure.basis.OccupationBasis class method) (kmcpy.structure.cluster.Cluster class method) (kmcpy.structure.cluster.Orbit class method) (kmcpy.structure.comparator.SupercellComparator class method) (kmcpy.structure.local_site_order.LocalSiteOrder class method) validate_reference_lattice_structure() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) validate_schedule() (in module kmcpy.simulator.property) values (kmcpy.structure.basis.Occupation property) volume (kmcpy.simulator.tracker.Tracker property)

W

which_config() (kmcpy.simulator.config.Configuration method) with_exclude_center_site() (kmcpy.structure.local_site_order.LocalSiteOrder method) with_runtime_changes() (kmcpy.simulator.config.Configuration method) with_system_changes() (kmcpy.simulator.config.Configuration method) with_traceback() (kmcpy.simulator.tracker.CallbackExecutionError method)

write_fitting_inputs() (kmcpy.io.neb.data.NEBDataLoader method) (kmcpy.io.neb.NEBDataLoader method) write_representative_clusters() (kmcpy.models.local_cluster_expansion.LocalClusterExpansion method) write_results() (kmcpy.simulator.tracker.Tracker method) write_template() (in module kmcpy.cli.init) write_tracker_results() (in module kmcpy.simulator.results)

Z

zeros() (kmcpy.structure.basis.Occupation class method)