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

Package for diffusion analysis.