pymatgen.analysis namespace

Subpackages

• pymatgen.analysis.diffusion package
  • Subpackages
    • pymatgen.analysis.diffusion.aimd package
      • Subpackages
      • Submodules
        • pymatgen.analysis.diffusion.aimd.clustering module
          • Kmeans
            • Kmeans.cluster()
            • Kmeans.get_centroids()
            • Kmeans.get_labels()
            • Kmeans.should_stop()
          • KmeansPBC
            • KmeansPBC.get_centroids()
            • KmeansPBC.get_labels()
            • KmeansPBC.should_stop()
          • get_random_centroid()
          • get_random_centroids()
        • pymatgen.analysis.diffusion.aimd.pathway module
          • ProbabilityDensityAnalysis
            • ProbabilityDensityAnalysis.from_diffusion_analyzer()
            • ProbabilityDensityAnalysis.generate_stable_sites()
            • ProbabilityDensityAnalysis.get_full_structure()
            • ProbabilityDensityAnalysis.to_chgcar()
          • SiteOccupancyAnalyzer
            • SiteOccupancyAnalyzer.site_occ
            • SiteOccupancyAnalyzer.coords_ref
            • SiteOccupancyAnalyzer.nsites
            • SiteOccupancyAnalyzer.structure
            • SiteOccupancyAnalyzer.from_diffusion_analyzer()
            • SiteOccupancyAnalyzer.get_average_site_occupancy()
        • pymatgen.analysis.diffusion.aimd.rdf module
          • RadialDistributionFunction
            • RadialDistributionFunction.coordination_number
            • RadialDistributionFunction.export_rdf()
            • RadialDistributionFunction.from_species()
            • RadialDistributionFunction.get_rdf_plot()
          • RadialDistributionFunctionFast
            • RadialDistributionFunctionFast.get_coordination_number()
            • RadialDistributionFunctionFast.get_one_rdf()
            • RadialDistributionFunctionFast.get_rdf()
        • pymatgen.analysis.diffusion.aimd.van_hove module
          • EvolutionAnalyzer
            • EvolutionAnalyzer.atom_dist()
            • EvolutionAnalyzer.get_df()
            • EvolutionAnalyzer.get_min_dist()
            • EvolutionAnalyzer.get_pairs()
            • EvolutionAnalyzer.plot_atomic_evolution()
            • EvolutionAnalyzer.plot_evolution_from_data()
            • EvolutionAnalyzer.plot_rdf_evolution()
            • EvolutionAnalyzer.rdf()
          • VanHoveAnalysis
            • VanHoveAnalysis.get_1d_plot()
            • VanHoveAnalysis.get_3d_plot()
      • Module contents
    • pymatgen.analysis.diffusion.neb package
      • Subpackages
      • Submodules
        • pymatgen.analysis.diffusion.neb.full_path_mapper module
          • ChargeBarrierGraph
            • ChargeBarrierGraph.get_least_chg_path()
            • ChargeBarrierGraph.get_summary_dict()
            • ChargeBarrierGraph.populate_edges_with_chg_density_info()
          • MigrationGraph
            • MigrationGraph.add_data_to_similar_edges()
            • MigrationGraph.assign_cost_to_graph()
            • MigrationGraph.get_path()
            • MigrationGraph.get_structure_from_entries()
            • MigrationGraph.get_summary_dict()
            • MigrationGraph.host_structure
            • MigrationGraph.only_sites
            • MigrationGraph.symm_structure
            • MigrationGraph.unique_hops
            • MigrationGraph.with_base_structure()
            • MigrationGraph.with_distance()
            • MigrationGraph.with_local_env_strategy()
          • almost()
          • check_uc_hop()
          • generic_groupby()
          • get_hop_site_sequence()
          • get_only_sites_from_structure()
          • map_hop_sc2uc()
          • order_path()
        • pymatgen.analysis.diffusion.neb.io module
          • MVLCINEBEndPointSet
          • MVLCINEBSet
          • get_endpoint_dist()
          • get_endpoints_from_index()
        • pymatgen.analysis.diffusion.neb.pathfinder module
          • ChgcarPotential
          • DistinctPathFinder
            • DistinctPathFinder.get_paths()
            • DistinctPathFinder.write_all_paths()
          • FreeVolumePotential
          • IDPPSolver
            • IDPPSolver.from_endpoints()
            • IDPPSolver.get_unit_vector()
            • IDPPSolver.run()
          • MigrationHop
            • MigrationHop.get_sc_structures()
            • MigrationHop.get_structures()
            • MigrationHop.length
            • MigrationHop.write_path()
          • MixedPotential
          • NEBPathfinder
            • NEBPathfinder.images
            • NEBPathfinder.interpolate()
            • NEBPathfinder.plot_images()
            • NEBPathfinder.string_relax()
          • StaticPotential
            • StaticPotential.gaussian_smear()
            • StaticPotential.get_v()
            • StaticPotential.normalize()
            • StaticPotential.rescale_field()
        • pymatgen.analysis.diffusion.neb.periodic_dijkstra module
          • get_optimal_pathway_rev()
          • periodic_dijkstra()
          • periodic_dijkstra_on_sgraph()
      • Module contents
    • pymatgen.analysis.diffusion.utils package
      • Subpackages
      • Submodules
        • pymatgen.analysis.diffusion.utils.edge_data_from_sc module
          • add_edge_data_from_sc()
          • get_uc_pos()
          • get_unique_hop()
          • mh_eq()
        • pymatgen.analysis.diffusion.utils.maggma module
          • get_entries_from_dbs()
        • pymatgen.analysis.diffusion.utils.parse_entries module
          • get_inserted_on_base()
          • get_insertion_energy()
          • get_matched_structure_mapping()
          • get_sym_migration_ion_sites()
          • process_entries()
        • pymatgen.analysis.diffusion.utils.supercells module
          • get_sc_fromstruct()
          • get_start_end_structures()
      • Module contents
  • Submodules
    • pymatgen.analysis.diffusion.analyzer module
      • DiffusionAnalyzer
        • DiffusionAnalyzer.as_dict()
        • DiffusionAnalyzer.export_msdt()
        • DiffusionAnalyzer.from_dict()
        • DiffusionAnalyzer.from_files()
        • DiffusionAnalyzer.from_structures()
        • DiffusionAnalyzer.from_vaspruns()
        • DiffusionAnalyzer.get_drift_corrected_structures()
        • DiffusionAnalyzer.get_framework_rms_plot()
        • DiffusionAnalyzer.get_msd_plot()
        • DiffusionAnalyzer.get_summary_dict()
        • DiffusionAnalyzer.plot_msd()
      • fit_arrhenius()
      • get_arrhenius_plot()
      • get_conversion_factor()
      • get_diffusivity_from_msd()
      • get_extrapolated_conductivity()
      • get_extrapolated_diffusivity()
  • Module contents