Index

_

_icet (module)

_OrbitList (class in _icet)

A

acceptance_ratio (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) accepted_trials (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) add_equivalent_sites() (_icet.Orbit method) (icet.core.orbit.Orbit method) add_orbit() (_icet._OrbitList method) (icet.core.orbit_list.OrbitList method) add_structure() (icet.StructureContainer method) Advanced topics allowed_permutations (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute)

analyze_data() (in module mchammer.data_analysis) (mchammer.DataContainer method) append() (mchammer.DataContainer method) apply_observer() (mchammer.DataContainer method) ARDR ase_atoms_to_spglib_cell() (in module icet.tools.geometry) assert_structure_compatibility() (icet.ClusterSpace method) atomic_number_to_chemical_symbol() (in module icet.tools.geometry) atomic_numbers (_icet.Structure attribute) (icet.Structure attribute) attach_observer() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) available_properties (icet.StructureContainer attribute)

B

Background BaseOptimizer (class in icet.fitting.base_optimizer) BCC Bibliography BinaryShortRangeOrderObserver (class in mchammer.observers) boltzmann_constant (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute)

bootstrap (icet.fitting.EnsembleOptimizer attribute) build() (_icet.ManyBodyNeighborList method) (_icet.NeighborList method) (_icet.PermutationMatrix method) (icet.core.many_body_neighbor_list.ManyBodyNeighborList method)

C

C++ reference Cluster ClusterCounts ClusterSpace General LatticeSite LocalEnvironment LocalOrbitListGenerator ManyBodyNeighborList NeighborList Orbit OrbitList PeriodicTable PermutationMatrix Structure calculate_intersection() (_icet.ManyBodyNeighborList method) (icet.core.many_body_neighbor_list.ManyBodyNeighborList method) calculate_local_contribution() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.calculators.target_vector_calculator.TargetVectorCalculator method) calculate_total() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.calculators.target_vector_calculator.TargetVectorCalculator method) calculator (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) CanonicalAnnealing (class in mchammer.ensembles) CanonicalEnsemble (class in mchammer.ensembles) CE cell (_icet.Structure attribute) (icet.Structure attribute) CEs chemical_potentials (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) chemical_symbols (_icet.Structure attribute) (icet.ClusterSpace attribute) (icet.Structure attribute) chemical_symbols_to_numbers() (in module icet.tools.geometry) Class reference BinaryShortRangeOrderObserver C++ components CanonicalAnnealing CanonicalEnsemble ClusterCountObserver ClusterExpansion ClusterExpansionCalculator ClusterExpansionObserver ClusterSpace ConfigurationManager Convex hull CrossValidationEstimator DataContainer EnsembleOptimizer HybridEnsemble Optimizer Python core components Python/C++ interface SemiGrandCanonicalEnsemble SiteOccupancyObserver Structure Structure container Structure enumeration Structures TargetVectorCalculator Tools User interface; icet User interface; mchammer VCSGCEnsemble optimizers clear() (_icet._OrbitList method) (_icet.LocalOrbitListGenerator method) (icet.core.local_orbit_list_generator.LocalOrbitListGenerator method) (icet.core.orbit_list.OrbitList method) Cluster (C++ class) (class in _icet) (class in icet.core.cluster) Cluster expansion Construction Formalism Cluster size Cluster space Cluster::case1_min_indices (C++ function) Cluster::case2_min_indices (C++ function) Cluster::Cluster (C++ function), [1] Cluster::compare_sites_dists (C++ function) Cluster::distances (C++ function) Cluster::findMinimumClusterByBruteForce (C++ function) Cluster::findMinimumIndexPermutation (C++ function)

Cluster::getDistIndices (C++ function), [1] Cluster::getEqualMinimumFirstSites (C++ function) Cluster::getLocalEnvironment (C++ function) Cluster::getOrderFromFirstDists (C++ function) Cluster::getReorderedDistances (C++ function) Cluster::getReorderedSites (C++ function) Cluster::isCase2 (C++ function) Cluster::isEqualFirstDists (C++ function) Cluster::isSorted (C++ function) Cluster::order (C++ function) Cluster::print (C++ function) Cluster::radius (C++ function) Cluster::setTag (C++ function) Cluster::setThisOrder (C++ function) Cluster::sites (C++ function) Cluster::sort (C++ function) Cluster::swapSites (C++ function) Cluster::tag (C++ function) Cluster::validateSorting (C++ function) cluster_counts (icet.core.cluster_counts.ClusterCounts attribute) cluster_expansion (mchammer.calculators.ClusterExpansionCalculator attribute) cluster_space (icet.ClusterExpansion attribute), [1] (icet.StructureContainer attribute) ClusterCountObserver (class in mchammer.observers) ClusterCounts (C++ class) (class in _icet) (class in icet.core.cluster_counts) ClusterCounts::_clusterCounts (C++ member) ClusterCounts::ClusterCounts (C++ function) ClusterCounts::count (C++ function), [1] ClusterCounts::countCluster (C++ function) ClusterCounts::countLatticeSites (C++ function) ClusterCounts::countOrbitList (C++ function) ClusterCounts::getClusterCounts (C++ function) ClusterCounts::print (C++ function) ClusterCounts::reset (C++ function) ClusterCounts::size (C++ function) ClusterExpansion (class in icet) ClusterExpansionCalculator (class in mchammer.calculators) ClusterExpansionObserver (class in mchammer.observers) ClusterSpace (C++ class) (class in _icet) (class in icet) ClusterSpace::_multiComponentVectors (C++ member) ClusterSpace::_orbitList (C++ member) ClusterSpace::_sitePermutations (C++ member) ClusterSpace::ClusterSpace (C++ function), [1] ClusterSpace::evaluateClusterFunction (C++ function) ClusterSpace::evaluateClusterProduct (C++ function) ClusterSpace::getChemicalSymbols (C++ function) ClusterSpace::getClusterSpaceInfo (C++ function) ClusterSpace::getClusterSpaceSize (C++ function) ClusterSpace::getClusterVector (C++ function) ClusterSpace::getCutoffs (C++ function) ClusterSpace::getMultiComponentVectorPermutations (C++ function) ClusterSpace::getNativeClusters (C++ function) ClusterSpace::getNumberOfAllowedSpeciesBySite (C++ function) ClusterSpace::getOrbit (C++ function) ClusterSpace::getOrbitList (C++ function) ClusterSpace::getPrimitiveStructure (C++ function) ClusterSpace::getSpeciesMaps (C++ function) ClusterSpace::precomputeMultiComponentVectors (C++ function) ClusterSpace::pruneOrbitList (C++ function) compare_cluster_vectors() (in module mchammer.calculators.target_vector_calculator) Compressive sensing compute_rmse() (icet.fitting.base_optimizer.BaseOptimizer method) (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) concentrations (icet.tools.convex_hull.ConvexHull attribute) ConfigurationManager (class in mchammer) contributions_test (icet.fitting.Optimizer attribute) contributions_train (icet.fitting.Optimizer attribute) ConvexHull (class in icet.tools.convex_hull) copy() (icet.ClusterSpace method) count() (_icet.ClusterCounts method) (icet.core.cluster_counts.ClusterCounts method) count_lattice_neighbors() (_icet.ClusterCounts method) (icet.core.cluster_counts.ClusterCounts method) count_orbit_list() (_icet.ClusterCounts method) (icet.core.cluster_counts.ClusterCounts method) Credits Cross validation CrossValidationEstimator (class in icet.fitting) Crystal symmetry operation Cutoff cutoffs (icet.ClusterSpace attribute) CV

D

data (mchammer.DataContainer attribute) data_container (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) data_container_write_period (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) DataContainer (class in mchammer) DFT dimensions (icet.tools.convex_hull.ConvexHull attribute) distances (_icet.Cluster attribute) (icet.core.cluster.Cluster 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)

E

ECI ECIs energies (icet.tools.convex_hull.ConvexHull attribute) ensemble_parameters (mchammer.DataContainer attribute) (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) ensemble_size (icet.fitting.EnsembleOptimizer attribute) EnsembleOptimizer (class in icet.fitting) enumerate_structures() (in module icet.tools.structure_enumeration) enumerate_supercells() (in module icet.tools.structure_enumeration) equivalent_sites (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute)

error_matrix (icet.fitting.EnsembleOptimizer attribute) estimated_ground_state (mchammer.ensembles.CanonicalAnnealing attribute) estimated_ground_state_potential (mchammer.ensembles.CanonicalAnnealing attribute) evaluate_cluster_function() (_icet.ClusterSpace method) (icet.ClusterSpace method) Examples Cluster counts Cluster vectors Data container Mapping structures Special quasirandom structures Structure enumeration Structure mapping extract_low_energy_structures() (icet.tools.convex_hull.ConvexHull method)

F

FCC find_lattice_site_by_position() (_icet.Structure method) (icet.Structure method) (in module icet.tools.geometry) find_lattice_sites_by_positions() (_icet.Structure method) (icet.Structure method) find_site_by_position() (_icet.Structure method) (icet.Structure method) fit_method (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) fractional_to_cartesian() (in module icet.tools.geometry) from_atoms() (_icet.Structure class method) (icet.Structure class method) from_python() (_icet.Cluster method) (icet.core.cluster.Cluster method) Function reference C++ components ClusterExpansion ClusterExpansionCalculator ClusterSpace Convex hull DataContainer Python core components Python/C++ interface Structure Structure container Structure enumeration Structure mapping Structures TargetVectorCalculator Tools User interface; icet User interface; mchammer optimizers

G

generate_full_orbit_list() (_icet.LocalOrbitListGenerator method) (icet.core.local_orbit_list_generator.LocalOrbitListGenerator method) generate_local_orbit_list() (_icet.LocalOrbitListGenerator method) (icet.core.local_orbit_list_generator.LocalOrbitListGenerator method) generate_sqs() (in module icet.tools.structure_generation) generate_sqs_by_enumeration() (in module icet.tools.structure_generation) generate_target_structure() (in module icet.tools.structure_generation) get_all_possible_mc_vector_permutations() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_allowed_sites_permutations() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_atomic_numbers() (_icet.Structure method) (icet.Structure method) get_autocorrelation_function() (in module mchammer.data_analysis) get_average() (mchammer.DataContainer method) get_cell() (_icet.Structure method) (icet.Structure method) get_chemical_symbols() (_icet.ClusterSpace method) (_icet.Structure method) (icet.ClusterSpace method) (icet.Structure method) get_cluster_counts() (_icet.ClusterCounts method) (icet.core.cluster_counts.ClusterCounts method) get_cluster_space_info() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_cluster_space_size() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_cluster_vector() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_condition_number() (icet.StructureContainer method) get_contributions() (icet.fitting.base_optimizer.BaseOptimizer method) (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) get_correlation_length() (in module mchammer.data_analysis) get_cutoffs() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_data() (mchammer.DataContainer method) get_distance() (_icet.Structure method) (icet.Structure method) get_energy_at_convex_hull() (icet.tools.convex_hull.ConvexHull method) get_equivalent_sites() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_equivalent_sites_permutations() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_error_estimate() (in module mchammer.data_analysis) get_fit_data() (icet.StructureContainer method) get_flip_state() (mchammer.ConfigurationManager method) get_fractional_positions_from_neighbor_list() (in module icet.tools.geometry) get_indexed_positions() (_icet.PermutationMatrix method) get_mc_vectors() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_multi_component_vector_permutations() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_neighbor_lists() (in module icet.core.neighbor_list) get_neighbors() (_icet.NeighborList method)

get_number_of_allowed_species_by_site() (_icet.ClusterSpace method) (icet.ClusterSpace method) get_number_of_entries() (mchammer.DataContainer method) get_number_of_nbody_clusters() (_icet._OrbitList method) (icet.core.orbit_list.OrbitList method) get_number_of_orbits_by_order() (icet.ClusterSpace method) get_number_of_unique_offsets() (_icet.LocalOrbitListGenerator method) (icet.core.local_orbit_list_generator.LocalOrbitListGenerator 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_occupied_primitive_structure() (in module icet.tools.geometry) get_orbit() (_icet._OrbitList method) (_icet.ClusterSpace method) (icet.ClusterSpace method) (icet.core.orbit_list.OrbitList method) get_orbit_list() (_icet._OrbitList method) (icet.core.orbit_list.OrbitList method) get_pbc() (_icet.Structure method) (icet.Structure method) get_permutation() (in module icet.tools.geometry) get_permuted_positions() (_icet.PermutationMatrix method) get_position() (_icet.Structure method) (icet.Structure method) get_position_from_lattice_site() (in module icet.tools.geometry) get_positions() (_icet.Structure method) (icet.Structure method) get_possible_orbit_occupations() (icet.ClusterSpace method) get_primitive_structure() (_icet._OrbitList method) (icet.core.orbit_list.OrbitList method) (in module icet.tools.geometry) get_random_sublattice_index() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method) get_representative_cluster() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_representative_sites() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_scaled_positions() (in module icet.tools.geometry) get_singlet_info() (icet.core.cluster_space method) get_sites_with_permutation() (_icet.Orbit method) (icet.core.orbit.Orbit method) get_structure_indices() (icet.StructureContainer method) get_sublattices() (icet.ClusterSpace method) get_supercell_orbit_list() (icet.core.orbit_list.OrbitList method) get_swapped_state() (mchammer.ConfigurationManager method) get_symmetry_operations() (in module icet.tools.structure_enumeration) get_trajectory() (mchammer.DataContainer method) get_unique_site() (_icet.Structure method) (icet.Structure method) get_unique_sites() (_icet.Structure method) (icet.Structure method) Glossary

H

HybridEnsemble (class in mchammer.ensembles)

I

icet (C++ type) (module) icet.core.cluster (module) icet.core.cluster_counts (module) icet.core.cluster_space (module) icet.core.lattice_site (module) icet.core.local_orbit_list_generator (module) icet.core.many_body_neighbor_list (module) icet.core.neighbor_list (module) icet.core.orbit (module) icet.core.orbit_list (module) icet.core.permutation_matrix (module) icet.core.structure (module) icet.fitting (module) icet.fitting.base_optimizer (module) icet.tools.convex_hull (module) icet.tools.geometry (module) icet.tools.structure_enumeration (module)

icet.tools.structure_generation (module) icet.tools.structure_mapping (module) icet::getAllPermutations (C++ function) icet::getGeometricalRadius (C++ function) icet::getOffsetPositions (C++ function) icet::getPermutation (C++ function) icet::getPermutedVector (C++ function) icet::nextCartesianProduct (C++ function) icet::transformPosition (C++ function) index (_icet.LatticeSite attribute) Installation interval (mchammer.observers.BinaryShortRangeOrderObserver attribute) (mchammer.observers.ClusterCountObserver attribute) (mchammer.observers.ClusterExpansionObserver attribute) (mchammer.observers.SiteOccupancyObserver attribute) is_neighbor() (_icet.NeighborList method) is_supercell_self_correlated() (icet.ClusterSpace method) is_swap_possible() (mchammer.ConfigurationManager method)

K

kappa (mchammer.ensembles.VCSGCEnsemble attribute)

Kernel ridge regression

L

LASSO last_state (mchammer.DataContainer attribute) LatticeSite (C++ class) (class in _icet) LatticeSite::addUnitcellOffset (C++ function) LatticeSite::index (C++ function) LatticeSite::LatticeSite (C++ function), [1] LatticeSite::operator std::string (C++ function) LatticeSite::operator< (C++ function) LatticeSite::operator== (C++ function) LatticeSite::print (C++ function) LatticeSite::setIndex (C++ function) LatticeSite::setUnitcellOffset (C++ function) LatticeSite::unitcellOffset (C++ function) LocalEnvironment (C++ class) LocalEnvironment::getClusterIndices (C++ function) LocalEnvironment::getEquivalentIndices (C++ function) LocalEnvironment::getNeighborDistances (C++ function) LocalEnvironment::getNeighborIndices (C++ function) LocalEnvironment::getNeighborSites (C++ function) LocalEnvironment::index (C++ function)

LocalEnvironment::LocalEnvironment (C++ function), [1] LocalEnvironment::neighborDistances (C++ function) LocalEnvironment::neighborSites (C++ function) LocalEnvironment::operator std::string (C++ function) LocalEnvironment::print (C++ function) LocalEnvironment::setIndex (C++ function) LocalEnvironment::setNeighborDistances (C++ function) LocalEnvironment::setNeighborIndices (C++ function) LocalEnvironment::setNeighborSites (C++ function) LocalEnvironment::setSite (C++ function) LocalEnvironment::site (C++ function) LocalOrbitListGenerator (C++ class) (class in _icet) (class in icet.core.local_orbit_list_generator) LocalOrbitListGenerator::clear (C++ function) LocalOrbitListGenerator::getFullOrbitList (C++ function) LocalOrbitListGenerator::getLocalOrbitList (C++ function), [1] LocalOrbitListGenerator::getMapFromPrimitiveToSupercell (C++ function) LocalOrbitListGenerator::getNumberOfUniqueOffsets (C++ function) LocalOrbitListGenerator::getUniquePrimitiveCellOffsets (C++ function) LocalOrbitListGenerator::LocalOrbitListGenerator (C++ function), [1]

M

ManyBodyNeighborList (C++ class) (class in _icet) (class in icet.core.many_body_neighbor_list) ManyBodyNeighborList::addPairs (C++ function) ManyBodyNeighborList::addSinglet (C++ function) ManyBodyNeighborList::build (C++ function) ManyBodyNeighborList::combineToHigherOrder (C++ function) ManyBodyNeighborList::getIntersection (C++ function) ManyBodyNeighborList::getNumberOfSites (C++ function), [1] ManyBodyNeighborList::getSites (C++ function) ManyBodyNeighborList::ManyBodyNeighborList (C++ function) ManyBodyNeighborList::translateAllNi (C++ function) map_structure_to_reference() (in module icet.tools.structure_mapping) MC mchammer.calculators (module) mchammer.calculators.target_vector_calculator (module) mchammer.data_analysis (module) mchammer.ensembles (module)

mchammer.observers (module) metadata (mchammer.DataContainer attribute) Monte Carlo Calculators Canonical ensemble, [1] Cluster count observer Cluster expansion calculator Cluster expansion observer Configuration manager 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

N

n_nonzero_parameters (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) n_nonzero_parameters_splits (icet.fitting.CrossValidationEstimator attribute) n_parameters (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) n_splits (icet.fitting.CrossValidationEstimator attribute) n_steps (mchammer.ensembles.CanonicalAnnealing attribute) n_target_values (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute)

NeighborList (C++ class) (class in _icet) NeighborList::build (C++ function) NeighborList::cutoff (C++ function) NeighborList::getNeighbors (C++ function) NeighborList::isNeighbor (C++ function) NeighborList::NeighborList (C++ function) NeighborList::size (C++ function) NeighborList::update (C++ function)

O

observables (mchammer.DataContainer attribute) observer_interval (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) observers (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) occupations (mchammer.ConfigurationManager attribute) operator!= (C++ function) operator+ (C++ function), [1] operator+= (C++ function) operator- (C++ function) operator< (C++ function), [1], [2] operator== (C++ function), [1], [2] Optimization Optimizer (class in icet.fitting) Orbit (C++ class) (class in _icet) (class in icet.core.orbit) Orbit::_equivalentSites (C++ member) Orbit::_representativeCluster (C++ member) Orbit::addEquivalentSites (C++ function), [1] Orbit::contains (C++ function) Orbit::getAllowedSitesPermutations (C++ function) Orbit::getAllPossibleMultiComponentVectorPermutations (C++ function) Orbit::getClusterSize (C++ function) Orbit::getEquivalentSites (C++ function) Orbit::getMultiComponentVectors (C++ function) Orbit::getNumberOfDuplicates (C++ function) Orbit::getPermutationsOfEquivalentSites (C++ function) Orbit::getPermutedEquivalentSites (C++ function) Orbit::getRepresentativeCluster (C++ function) Orbit::getRepresentativeSites (C++ function) Orbit::GetSitesOfIndex (C++ function) Orbit::getSitesWithPermutation (C++ function) Orbit::operator+= (C++ function) Orbit::Orbit (C++ function) Orbit::radius (C++ function) Orbit::removeSites (C++ function) Orbit::removeSitesNotWithIndex (C++ function) Orbit::removeSitesWithIndex (C++ function) Orbit::setAllowedSitesPermutations (C++ function) Orbit::setEquivalentSites (C++ function) Orbit::setEquivalentSitesPermutations (C++ function) Orbit::size (C++ function) Orbit::sortOrbit (C++ function)

orbit_data (icet.ClusterSpace attribute) orbit_list (icet.ClusterSpace attribute) OrbitList (C++ class) (class in icet.core.orbit_list) OrbitList::_orbits (C++ member) OrbitList::addClusterToOrbitList (C++ function) OrbitList::addOrbit (C++ function) OrbitList::addOrbitFromPM (C++ function) OrbitList::addOrbitsFromPM (C++ function) OrbitList::addPermutationInformationToOrbits (C++ function) OrbitList::addPermutationMatrixColumns (C++ function) OrbitList::checkEquivalentClusters (C++ function) OrbitList::clear (C++ function) OrbitList::findRowsFromCol1 (C++ function) OrbitList::getAllColumnsFromRow (C++ function) OrbitList::getAllColumnsFromSites (C++ function) OrbitList::getColumn1FromPM (C++ function) OrbitList::getFirstColumnOfPermutationMatrix (C++ function) OrbitList::getLocalOrbitList (C++ function) OrbitList::getMatchesInPM (C++ function) OrbitList::getNumberOfNBodyClusters (C++ function) OrbitList::getOrbit (C++ function) OrbitList::getOrbits (C++ function) OrbitList::getPermutationMatrix (C++ function) OrbitList::getPrimitiveStructure (C++ function) OrbitList::getSitesTranslatedToUnitcell (C++ function) OrbitList::getSuperCellOrbit (C++ function) OrbitList::isRowsTaken (C++ function) OrbitList::isSitesPBCCorrect (C++ function) OrbitList::operator+= (C++ function) OrbitList::OrbitList (C++ function), [1] OrbitList::print (C++ function) OrbitList::removeInactiveOrbits (C++ function) OrbitList::removeOrbit (C++ function) OrbitList::removeSitesContainingIndex (C++ function) OrbitList::removeSitesNotContainingIndex (C++ function) OrbitList::setPrimitiveStructure (C++ function) OrbitList::size (C++ function) OrbitList::sort (C++ function) OrbitList::subtractSitesFromOrbitList (C++ function) OrbitList::transformSiteToSupercell (C++ function) OrbitList::translateSites (C++ function) OrbitList::validCluster (C++ function) Orbits orbits (_icet._OrbitList attribute) (icet.core.orbit_list.OrbitList attribute) order (_icet.Cluster attribute) (_icet.Orbit attribute) (icet.core.cluster.Cluster attribute) (icet.core.orbit.Orbit attribute) orders (icet.ClusterExpansion attribute)

P

parameter_vectors (icet.fitting.EnsembleOptimizer attribute) parameters (icet.ClusterExpansion attribute), [1] (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) (icet.fitting.base_optimizer.BaseOptimizer attribute) parameters_as_dataframe (icet.ClusterExpansion attribute) parameters_norm (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) parameters_splits (icet.fitting.CrossValidationEstimator attribute) parameters_std (icet.fitting.EnsembleOptimizer attribute) pbc (_icet.Structure attribute) (icet.Structure attribute) PeriodicTable (C++ type) PeriodicTable::intStr (C++ member) PeriodicTable::strInt (C++ member) permutation_matrix (_icet._OrbitList attribute) (icet.core.orbit_list.OrbitList attribute) permutation_matrix_from_structure() (in module icet.core.permutation_matrix) PermutationMatrix (C++ class) (class in _icet) PermutationMatrix::build (C++ function) PermutationMatrix::getIndexedPermutedPositions (C++ function)

PermutationMatrix::getPermutedPositions (C++ function) PermutationMatrix::PermutationMatrix (C++ function) permutations_to_representative (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute) permuted_sites (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute) phis (mchammer.ensembles.VCSGCEnsemble attribute) plot_parameters() (icet.ClusterExpansion method) positions (_icet.Structure attribute) (icet.Structure attribute) predict() (icet.ClusterExpansion method) (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) (icet.fitting.base_optimizer.BaseOptimizer method) primitive_structure (icet.ClusterSpace attribute) (icet.core.orbit_list.OrbitList attribute) print() (_icet.Cluster method) (_icet.LatticeSite method) (icet.core.cluster.Cluster method) print_overview() (icet.ClusterExpansion method) (icet.ClusterSpace method) (icet.StructureContainer method) probabilities (mchammer.ensembles.HybridEnsemble attribute) prune() (icet.ClusterExpansion method)

R

radius (_icet.Cluster attribute) (_icet.Orbit attribute) (icet.core.cluster.Cluster attribute) (icet.core.orbit.Orbit attribute) random_seed (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) read() (icet.ClusterExpansion static method) (icet.ClusterSpace static method) (icet.StructureContainer static method) (mchammer.DataContainer static method) Regularization remove_inactive_orbits() (icet.core.orbit_list.OrbitList method) remove_orbit() (_icet._OrbitList method) (icet.core.orbit_list.OrbitList method) representative_cluster (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute) representative_sites (_icet.Orbit attribute) (icet.core.orbit.Orbit attribute) reset() (_icet.ClusterCounts method) (icet.core.cluster_counts.ClusterCounts method) (mchammer.DataContainer method) reset_data_container() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method)

return_type (mchammer.observers.BinaryShortRangeOrderObserver attribute) (mchammer.observers.ClusterCountObserver attribute) (mchammer.observers.ClusterExpansionObserver attribute) (mchammer.observers.SiteOccupancyObserver attribute) RFE rmse_test (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) rmse_test_ensemble (icet.fitting.EnsembleOptimizer attribute) rmse_train (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) rmse_train_ensemble (icet.fitting.EnsembleOptimizer attribute) rmse_train_final (icet.fitting.CrossValidationEstimator attribute) rmse_train_splits (icet.fitting.CrossValidationEstimator attribute) rmse_validation (icet.fitting.CrossValidationEstimator attribute) rmse_validation_splits (icet.fitting.CrossValidationEstimator attribute) run() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method)

S

seed (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) SemiGrandCanonicalEnsemble (class in mchammer.ensembles) set_atomic_numbers() (_icet.Structure method) (icet.Structure method) set_cell() (_icet.Structure method) (icet.Structure method) set_chemical_symbols() (_icet.Structure method) (icet.Structure method) set_number_of_allowed_species() (_icet.Structure method) (icet.Structure method) set_pbc() (_icet.Structure method) (icet.Structure method) set_positions() (_icet.Structure method) (icet.Structure method) set_unique_sites() (_icet.Structure method) (icet.Structure method) SiteOccupancyObserver (class in mchammer.observers) sites (_icet.Cluster attribute) (icet.core.cluster.Cluster attribute) sort() (_icet._OrbitList method) (_icet.Orbit method) (icet.core.orbit.Orbit method) (icet.core.orbit_list.OrbitList method) sorted (_icet.Cluster attribute) (icet.core.cluster.Cluster attribute) species_maps (_icet.ClusterSpace attribute) (icet.ClusterSpace attribute) standardize (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute) Structure (C++ class) (class in _icet) (class in icet) structure (mchammer.calculators.ClusterExpansionCalculator attribute) (mchammer.ConfigurationManager attribute) (mchammer.calculators.target_vector_calculator.TargetVectorCalculator attribute) (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute)

Structure::_atomicNumbers (C++ member) Structure::findLatticeSiteByPosition (C++ function) Structure::findLatticeSitesByPositions (C++ function) Structure::findSiteByPosition (C++ function) Structure::getAtomicNumber (C++ function) Structure::getAtomicNumbers (C++ function) Structure::getCell (C++ function) Structure::getChemicalSymbols (C++ function) Structure::getDistance (C++ function) Structure::getNumberOfAllowedSpeciesBySite (C++ function) Structure::getNumberOfAllowedSpeciesBySites (C++ function) Structure::getPBC (C++ function) Structure::getPosition (C++ function) Structure::getPositionByIndex (C++ function) Structure::getPositions (C++ function) Structure::getTolerance (C++ function) Structure::getUniqueSite (C++ function) Structure::getUniqueSites (C++ function) Structure::hasPBC (C++ function) Structure::setAtomicNumbers (C++ function) Structure::setCell (C++ function) Structure::setChemicalSymbols (C++ function) Structure::setNumberOfAllowedSpecies (C++ function), [1] Structure::setPBC (C++ function) Structure::setPositions (C++ function) Structure::setTolerance (C++ function) Structure::setUniqueSites (C++ function) Structure::size (C++ function) Structure::Structure (C++ function), [1] StructureContainer (class in icet) structures (icet.tools.convex_hull.ConvexHull attribute) sublattices (mchammer.calculators.ClusterExpansionCalculator attribute) (mchammer.ConfigurationManager attribute) (mchammer.calculators.target_vector_calculator.TargetVectorCalculator attribute) (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) summary (icet.fitting.base_optimizer.BaseOptimizer attribute) (icet.fitting.CrossValidationEstimator attribute) (icet.fitting.EnsembleOptimizer attribute) (icet.fitting.Optimizer attribute)

T

T_start (mchammer.ensembles.CanonicalAnnealing attribute) T_stop (mchammer.ensembles.CanonicalAnnealing attribute) tag (_icet.Cluster attribute) (icet.core.cluster.Cluster attribute) (mchammer.observers.BinaryShortRangeOrderObserver attribute) (mchammer.observers.ClusterCountObserver attribute) (mchammer.observers.ClusterExpansionObserver attribute) (mchammer.observers.SiteOccupancyObserver attribute) TargetVectorCalculator (class in mchammer.calculators.target_vector_calculator) temperature (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute) test_fraction (icet.fitting.Optimizer attribute) test_scatter_data (icet.fitting.Optimizer attribute) test_set (icet.fitting.Optimizer attribute) test_size (icet.fitting.Optimizer attribute) to_atoms() (_icet.Structure method) (icet.Structure method) total_trials (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute)

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

U

unique_sites (_icet.Structure attribute) (icet.Structure attribute) unitcell_offset (_icet.LatticeSite attribute) update_occupations() (mchammer.calculators.ClusterExpansionCalculator method) (mchammer.ConfigurationManager method) (mchammer.calculators.target_vector_calculator.TargetVectorCalculator method) (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method)

user_tag (mchammer.ensembles.CanonicalAnnealing attribute) (mchammer.ensembles.CanonicalEnsemble attribute) (mchammer.ensembles.HybridEnsemble attribute) (mchammer.ensembles.SemiGrandCanonicalEnsemble attribute) (mchammer.ensembles.VCSGCEnsemble attribute)

V

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

validation_scatter_data (icet.fitting.CrossValidationEstimator attribute) VCSGCEnsemble (class in mchammer.ensembles) view_singlets() (icet.core.cluster_space method)

W

Workflow write() (icet.ClusterExpansion method) (icet.ClusterSpace method) (icet.StructureContainer method) (mchammer.DataContainer method) write_data_container() (mchammer.ensembles.CanonicalAnnealing method) (mchammer.ensembles.CanonicalEnsemble method) (mchammer.ensembles.HybridEnsemble method) (mchammer.ensembles.SemiGrandCanonicalEnsemble method) (mchammer.ensembles.VCSGCEnsemble method)

write_summary() (icet.fitting.base_optimizer.BaseOptimizer method) (icet.fitting.CrossValidationEstimator method) (icet.fitting.EnsembleOptimizer method) (icet.fitting.Optimizer method) write_trajectory() (mchammer.DataContainer method)