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

Analysis tools for NEB calculations, including pathway analysis.