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

Modules for AIMD simulation analysis.