Index

A

add_data_to_similar_edges() (MigrationGraph method) add_edge_data_from_sc() (in module pymatgen.analysis.diffusion.utils.edge_data_from_sc) almost() (in module pymatgen.analysis.diffusion.neb.full_path_mapper)

as_dict() (DiffusionAnalyzer method) assign_cost_to_graph() (MigrationGraph method) atom_dist() (EvolutionAnalyzer static method)

C

ChargeBarrierGraph (class in pymatgen.analysis.diffusion.neb.full_path_mapper) ChargeBarrierGraphTest (class in pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper) check_uc_hop() (in module pymatgen.analysis.diffusion.neb.full_path_mapper)

ChgcarPotential (class in pymatgen.analysis.diffusion.neb.pathfinder) cluster() (Kmeans method) coordination_number (RadialDistributionFunction property) coords_ref (SiteOccupancyAnalyzer attribute)

D

DiffusionAnalyzer (class in pymatgen.analysis.diffusion.analyzer) DiffusionAnalyzerTest (class in pymatgen.analysis.diffusion.tests.test_analyzer)

DistinctPathFinder (class in pymatgen.analysis.diffusion.neb.pathfinder) DistinctPathFinderTest (class in pymatgen.analysis.diffusion.neb.tests.test_pathfinder)

E

endpoint (MVLCINEBEndPointSetTest attribute) EvolutionAnalyzer (class in pymatgen.analysis.diffusion.aimd.van_hove)

EvolutionAnalyzerTest (class in pymatgen.analysis.diffusion.aimd.tests.test_van_hove) export_msdt() (DiffusionAnalyzer method) export_rdf() (RadialDistributionFunction method)

F

final_struct (IDPPSolverTest attribute) fit_arrhenius() (in module pymatgen.analysis.diffusion.analyzer) FreeVolumePotential (class in pymatgen.analysis.diffusion.neb.pathfinder) from_dict() (DiffusionAnalyzer class method) from_diffusion_analyzer() (ProbabilityDensityAnalysis class method) (SiteOccupancyAnalyzer class method)

from_endpoints() (IDPPSolver class method) from_files() (DiffusionAnalyzer class method) from_species() (RadialDistributionFunction class method) from_structures() (DiffusionAnalyzer class method) from_vaspruns() (DiffusionAnalyzer class method) FuncTest (class in pymatgen.analysis.diffusion.tests.test_analyzer)

G

gaussian_smear() (StaticPotential method) generate_stable_sites() (ProbabilityDensityAnalysis method) generic_groupby() (in module pymatgen.analysis.diffusion.neb.full_path_mapper) get_1d_plot() (VanHoveAnalysis method) get_3d_plot() (VanHoveAnalysis method) get_arrhenius_plot() (in module pymatgen.analysis.diffusion.analyzer) get_average_site_occupancy() (SiteOccupancyAnalyzer method) get_centroids() (Kmeans static method) (KmeansPBC method) get_conversion_factor() (in module pymatgen.analysis.diffusion.analyzer) get_coordination_number() (RadialDistributionFunctionFast method) get_df() (EvolutionAnalyzer method) get_diffusivity_from_msd() (in module pymatgen.analysis.diffusion.analyzer) get_drift_corrected_structures() (DiffusionAnalyzer method) get_endpoint_dist() (in module pymatgen.analysis.diffusion.neb.io) get_endpoints_from_index() (in module pymatgen.analysis.diffusion.neb.io) get_entries_from_dbs() (in module pymatgen.analysis.diffusion.utils.maggma) get_extrapolated_conductivity() (in module pymatgen.analysis.diffusion.analyzer) get_extrapolated_diffusivity() (in module pymatgen.analysis.diffusion.analyzer) get_framework_rms_plot() (DiffusionAnalyzer method) get_full_structure() (ProbabilityDensityAnalysis method) get_hop_site_sequence() (in module pymatgen.analysis.diffusion.neb.full_path_mapper) get_inserted_on_base() (in module pymatgen.analysis.diffusion.utils.parse_entries) get_insertion_energy() (in module pymatgen.analysis.diffusion.utils.parse_entries) get_labels() (Kmeans static method) (KmeansPBC method) get_least_chg_path() (ChargeBarrierGraph method)

get_matched_structure_mapping() (in module pymatgen.analysis.diffusion.utils.parse_entries) get_min_dist() (EvolutionAnalyzer static method) get_msd_plot() (DiffusionAnalyzer method) get_one_rdf() (RadialDistributionFunctionFast method) get_only_sites_from_structure() (in module pymatgen.analysis.diffusion.neb.full_path_mapper) get_optimal_pathway_rev() (in module pymatgen.analysis.diffusion.neb.periodic_dijkstra) get_pairs() (EvolutionAnalyzer static method) get_path() (in module pymatgen.analysis.diffusion.neb.tests.test_io) (in module pymatgen.analysis.diffusion.neb.tests.test_pathfinder) (MigrationGraph method) get_paths() (DistinctPathFinder method) get_random_centroid() (in module pymatgen.analysis.diffusion.aimd.clustering) get_random_centroids() (in module pymatgen.analysis.diffusion.aimd.clustering) get_rdf() (RadialDistributionFunctionFast method) get_rdf_plot() (RadialDistributionFunction method) get_sc_fromstruct() (in module pymatgen.analysis.diffusion.utils.supercells) get_sc_structures() (MigrationHop method) get_start_end_structures() (in module pymatgen.analysis.diffusion.utils.supercells) get_structure_from_entries() (MigrationGraph static method) get_structures() (MigrationHop method) get_summary_dict() (ChargeBarrierGraph method) (DiffusionAnalyzer method) (MigrationGraph method) get_sym_migration_ion_sites() (in module pymatgen.analysis.diffusion.utils.parse_entries) get_uc_pos() (in module pymatgen.analysis.diffusion.utils.edge_data_from_sc) get_unique_hop() (in module pymatgen.analysis.diffusion.utils.edge_data_from_sc) get_unit_vector() (IDPPSolver static method) get_v() (StaticPotential method)

H

host_structure (MigrationGraph property)

I

IDPPSolver (class in pymatgen.analysis.diffusion.neb.pathfinder) IDPPSolverTest (class in pymatgen.analysis.diffusion.neb.tests.test_pathfinder)

images (NEBPathfinder property) init_struct (IDPPSolverTest attribute) interpolate() (NEBPathfinder method)

K

Kmeans (class in pymatgen.analysis.diffusion.aimd.clustering) KmeansPBC (class in pymatgen.analysis.diffusion.aimd.clustering)

KmeansPBCTest (class in pymatgen.analysis.diffusion.aimd.tests.test_clustering) KmeansTest (class in pymatgen.analysis.diffusion.aimd.tests.test_clustering)

L

length (MigrationHop property)

M

map_hop_sc2uc() (in module pymatgen.analysis.diffusion.neb.full_path_mapper) mh_eq() (in module pymatgen.analysis.diffusion.utils.edge_data_from_sc) MigrationGraph (class in pymatgen.analysis.diffusion.neb.full_path_mapper) MigrationGraphComplexTest (class in pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper) MigrationGraphFromEntriesTest (class in pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper) MigrationGraphSimpleTest (class in pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper) MigrationHop (class in pymatgen.analysis.diffusion.neb.pathfinder) MigrationHopTest (class in pymatgen.analysis.diffusion.neb.tests.test_pathfinder) MixedPotential (class in pymatgen.analysis.diffusion.neb.pathfinder) module pymatgen pymatgen.analysis pymatgen.analysis.diffusion pymatgen.analysis.diffusion.aimd pymatgen.analysis.diffusion.aimd.clustering pymatgen.analysis.diffusion.aimd.pathway pymatgen.analysis.diffusion.aimd.rdf pymatgen.analysis.diffusion.aimd.tests.test_clustering pymatgen.analysis.diffusion.aimd.tests.test_pathway pymatgen.analysis.diffusion.aimd.tests.test_rdf pymatgen.analysis.diffusion.aimd.tests.test_van_hove pymatgen.analysis.diffusion.aimd.van_hove pymatgen.analysis.diffusion.analyzer pymatgen.analysis.diffusion.neb pymatgen.analysis.diffusion.neb.full_path_mapper pymatgen.analysis.diffusion.neb.io pymatgen.analysis.diffusion.neb.pathfinder pymatgen.analysis.diffusion.neb.periodic_dijkstra pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper pymatgen.analysis.diffusion.neb.tests.test_io pymatgen.analysis.diffusion.neb.tests.test_pathfinder pymatgen.analysis.diffusion.tests.test_analyzer pymatgen.analysis.diffusion.tests.test_pathfinder pymatgen.analysis.diffusion.utils pymatgen.analysis.diffusion.utils.edge_data_from_sc pymatgen.analysis.diffusion.utils.maggma pymatgen.analysis.diffusion.utils.parse_entries pymatgen.analysis.diffusion.utils.supercells pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc pymatgen.analysis.diffusion.utils.tests.test_parse_entries

MVLCINEBEndPointSet (class in pymatgen.analysis.diffusion.neb.io) MVLCINEBEndPointSetTest (class in pymatgen.analysis.diffusion.neb.tests.test_io) MVLCINEBSet (class in pymatgen.analysis.diffusion.neb.io) MVLCINEBSetTest (class in pymatgen.analysis.diffusion.neb.tests.test_io)

N

NEBPathfinder (class in pymatgen.analysis.diffusion.neb.pathfinder)

normalize() (StaticPotential method) nsites (SiteOccupancyAnalyzer attribute)

O

only_sites (MigrationGraph property)

order_path() (in module pymatgen.analysis.diffusion.neb.full_path_mapper)

P

ParseEntriesTest (class in pymatgen.analysis.diffusion.utils.tests.test_parse_entries) PathfinderTest (class in pymatgen.analysis.diffusion.tests.test_pathfinder) periodic_dijkstra() (in module pymatgen.analysis.diffusion.neb.periodic_dijkstra) periodic_dijkstra_on_sgraph() (in module pymatgen.analysis.diffusion.neb.periodic_dijkstra) plot_atomic_evolution() (EvolutionAnalyzer method) plot_evolution_from_data() (EvolutionAnalyzer static method) plot_images() (NEBPathfinder method) plot_msd() (DiffusionAnalyzer method) plot_rdf_evolution() (EvolutionAnalyzer method) populate_edges_with_chg_density_info() (ChargeBarrierGraph method) ProbabilityDensityAnalysis (class in pymatgen.analysis.diffusion.aimd.pathway) ProbabilityDensityTest (class in pymatgen.analysis.diffusion.aimd.tests.test_pathway) process_entries() (in module pymatgen.analysis.diffusion.utils.parse_entries) pymatgen module pymatgen.analysis module pymatgen.analysis.diffusion module pymatgen.analysis.diffusion.aimd module pymatgen.analysis.diffusion.aimd.clustering module pymatgen.analysis.diffusion.aimd.pathway module pymatgen.analysis.diffusion.aimd.rdf module pymatgen.analysis.diffusion.aimd.tests.test_clustering module pymatgen.analysis.diffusion.aimd.tests.test_pathway module pymatgen.analysis.diffusion.aimd.tests.test_rdf module pymatgen.analysis.diffusion.aimd.tests.test_van_hove module pymatgen.analysis.diffusion.aimd.van_hove module

pymatgen.analysis.diffusion.analyzer module pymatgen.analysis.diffusion.neb module pymatgen.analysis.diffusion.neb.full_path_mapper module pymatgen.analysis.diffusion.neb.io module pymatgen.analysis.diffusion.neb.pathfinder module pymatgen.analysis.diffusion.neb.periodic_dijkstra module pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module pymatgen.analysis.diffusion.neb.tests.test_io module pymatgen.analysis.diffusion.neb.tests.test_pathfinder module pymatgen.analysis.diffusion.tests.test_analyzer module pymatgen.analysis.diffusion.tests.test_pathfinder module pymatgen.analysis.diffusion.utils module pymatgen.analysis.diffusion.utils.edge_data_from_sc module pymatgen.analysis.diffusion.utils.maggma module pymatgen.analysis.diffusion.utils.parse_entries module pymatgen.analysis.diffusion.utils.supercells module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module pymatgen.analysis.diffusion.utils.tests.test_parse_entries module

R

RadialDistributionFunction (class in pymatgen.analysis.diffusion.aimd.rdf) RadialDistributionFunctionFast (class in pymatgen.analysis.diffusion.aimd.rdf) rdf() (EvolutionAnalyzer static method)

RDFTest (class in pymatgen.analysis.diffusion.aimd.tests.test_rdf) (class in pymatgen.analysis.diffusion.aimd.tests.test_van_hove) rescale_field() (StaticPotential method) run() (IDPPSolver method)

S

setUp() (ChargeBarrierGraphTest method) (MigrationGraphComplexTest method) (MigrationGraphFromEntriesTest method) (MigrationGraphSimpleTest method) (MigrationHopTest method) (ParseEntriesTest method) (RDFTest method) should_stop() (Kmeans method) (KmeansPBC method)

site_occ (SiteOccupancyAnalyzer attribute) SiteOccupancyAnalyzer (class in pymatgen.analysis.diffusion.aimd.pathway) SiteOccupancyTest (class in pymatgen.analysis.diffusion.aimd.tests.test_pathway) StaticPotential (class in pymatgen.analysis.diffusion.neb.pathfinder) string_relax() (NEBPathfinder static method) structure (SiteOccupancyAnalyzer attribute) (UtilityTest attribute) structures (MVLCINEBSetTest attribute) symm_structure (MigrationGraph property)

T

test_add_data_to_similar_edges() (MigrationGraphComplexTest method) test_add_edge_data_from_sc() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc) test_assign_cost_to_graph() (MigrationGraphComplexTest method) test_cluster() (KmeansPBCTest method) (KmeansTest method) test_filter_and_merge() (ParseEntriesTest method) test_fit_arrhenius() (FuncTest method) test_from_structure_NPT() (DiffusionAnalyzerTest method) test_generate_stable_sites() (ProbabilityDensityTest method) test_get_all_sym_sites() (ParseEntriesTest method) test_get_conversion_factor() (FuncTest method) test_get_df() (EvolutionAnalyzerTest method) test_get_endpoint_dist() (UtilityTest method) test_get_endpoints_from_index() (UtilityTest method) test_get_inserted_on_base() (ParseEntriesTest method) test_get_insertion_energy() (ParseEntriesTest method) test_get_key_in_path() (MigrationGraphComplexTest method) test_get_path() (MigrationGraphComplexTest method) test_get_paths() (DistinctPathFinderTest method) test_get_pos_and_migration_hop() (MigrationGraphSimpleTest method) test_get_sc_structures() (MigrationHopTest method) test_get_sc_structures_vacmode() (MigrationHopTest method) test_get_start_end_structs_from_hop() (MigrationHopTest method) test_get_start_end_structs_from_hop_vac() (MigrationHopTest method) test_get_summary_dict() (ChargeBarrierGraphTest method) (MigrationGraphSimpleTest method) test_get_uc_pos() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc) test_get_unique_hop_host() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc) test_get_unique_host_nonhost() (in module pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc) test_group_and_label_hops() (MigrationGraphComplexTest method) test_idpp() (IDPPSolverTest method) test_idpp_from_ep() (IDPPSolverTest method)

test_idpp_from_ep_diff_latt() (IDPPSolverTest method) test_incar() (MVLCINEBEndPointSetTest method) (MVLCINEBSetTest method) test_incar_user_setting() (MVLCINEBEndPointSetTest method) (MVLCINEBSetTest method) test_init() (DiffusionAnalyzerTest method) test_init_npt() (DiffusionAnalyzerTest method) test_integration() (ChargeBarrierGraphTest method) test_m_graph_construction() (MigrationGraphFromEntriesTest method) test_m_graph_from_entries_failed() (MigrationGraphFromEntriesTest method) test_max_path_length() (DistinctPathFinderTest method) test_mhop_msonable() (PathfinderTest method) test_msonable() (MigrationHopTest method) test_not_matching_first() (MigrationGraphComplexTest method) test_order_path() (MigrationGraphComplexTest method) test_periodic_dijkstra() (MigrationGraphComplexTest method) test_populate_edges_with_chg_density_info() (ChargeBarrierGraphTest method) test_probability() (ProbabilityDensityTest method) test_probability_classmethod() (ProbabilityDensityTest method) test_process_ents() (ParseEntriesTest method) test_raises_valueerror_if_ngrid_is_less_than_2() (RDFTest method) test_raises_ValueError_if_reference_species_not_in_structure() (RDFTest method) test_raises_ValueError_if_sigma_is_not_positive() (RDFTest method) test_raises_ValueError_if_species_not_in_structure() (RDFTest method) test_rdf() (RDFTest method), [1] test_rdf_coordination_number() (RDFTest method), [1] test_rdf_two_species_coordination_number() (RDFTest method) test_site_occupancy() (SiteOccupancyTest method) test_site_occupancy_classmethod() (SiteOccupancyTest method) test_to_chgcar() (ProbabilityDensityTest method) test_unique_hops_dict() (MigrationGraphComplexTest method) test_van_hove() (VanHoveTest method) to_chgcar() (ProbabilityDensityAnalysis method)

U

unique_hops (MigrationGraph property)

UtilityTest (class in pymatgen.analysis.diffusion.neb.tests.test_io)

V

VanHoveAnalysis (class in pymatgen.analysis.diffusion.aimd.van_hove)

VanHoveTest (class in pymatgen.analysis.diffusion.aimd.tests.test_van_hove)

W

with_base_structure() (MigrationGraph class method) with_distance() (MigrationGraph class method)

with_local_env_strategy() (MigrationGraph class method) write_all_paths() (DistinctPathFinder method) write_path() (MigrationHop method)