├── .coverage ├── .github ├── dependabot.yml └── workflows │ ├── lint.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGES.rst ├── COPYRIGHT ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── .nojekyll ├── _modules │ ├── index.html │ ├── pymatgen │ │ └── analysis │ │ │ └── diffusion │ │ │ ├── aimd │ │ │ ├── clustering.html │ │ │ ├── pathway.html │ │ │ ├── rdf.html │ │ │ ├── tests │ │ │ │ ├── test_clustering.html │ │ │ │ ├── test_pathway.html │ │ │ │ ├── test_rdf.html │ │ │ │ └── test_van_hove.html │ │ │ └── van_hove.html │ │ │ ├── analyzer.html │ │ │ ├── neb │ │ │ ├── full_path_mapper.html │ │ │ ├── io.html │ │ │ ├── pathfinder.html │ │ │ ├── periodic_dijkstra.html │ │ │ └── tests │ │ │ │ ├── test_full_path_mapper.html │ │ │ │ ├── test_io.html │ │ │ │ └── test_pathfinder.html │ │ │ ├── tests │ │ │ ├── test_analyzer.html │ │ │ └── test_pathfinder.html │ │ │ └── utils │ │ │ ├── edge_data_from_sc.html │ │ │ ├── maggma.html │ │ │ ├── parse_entries.html │ │ │ ├── supercells.html │ │ │ └── tests │ │ │ ├── test_edge_data_from_sc.html │ │ │ ├── test_maggma.html │ │ │ └── test_parse_entries.html │ └── pymatgen_diffusion │ │ ├── aimd │ │ ├── clustering.html │ │ ├── pathway.html │ │ ├── rdf.html │ │ └── van_hove.html │ │ └── neb │ │ ├── full_path_mapper.html │ │ ├── io.html │ │ ├── pathfinder.html │ │ └── periodic_dijkstra.html ├── _sources │ ├── _themes │ │ └── README.rst.txt │ ├── change_log.rst.txt │ ├── index.rst.txt │ ├── modules.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.clustering.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.pathway.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.rdf.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.tests.test_clustering.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.tests.test_pathway.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.tests.test_rdf.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.tests.test_van_hove.rst.txt │ ├── pymatgen.analysis.diffusion.aimd.van_hove.rst.txt │ ├── pymatgen.analysis.diffusion.analyzer.rst.txt │ ├── pymatgen.analysis.diffusion.neb.full_path_mapper.rst.txt │ ├── pymatgen.analysis.diffusion.neb.io.rst.txt │ ├── pymatgen.analysis.diffusion.neb.pathfinder.rst.txt │ ├── pymatgen.analysis.diffusion.neb.periodic_dijkstra.rst.txt │ ├── pymatgen.analysis.diffusion.neb.rst.txt │ ├── pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.rst.txt │ ├── pymatgen.analysis.diffusion.neb.tests.test_io.rst.txt │ ├── pymatgen.analysis.diffusion.neb.tests.test_pathfinder.rst.txt │ ├── pymatgen.analysis.diffusion.rst.txt │ ├── pymatgen.analysis.diffusion.tests.test_analyzer.rst.txt │ ├── pymatgen.analysis.diffusion.tests.test_pathfinder.rst.txt │ ├── pymatgen.analysis.diffusion.utils.edge_data_from_sc.rst.txt │ ├── pymatgen.analysis.diffusion.utils.maggma.rst.txt │ ├── pymatgen.analysis.diffusion.utils.parse_entries.rst.txt │ ├── pymatgen.analysis.diffusion.utils.rst.txt │ ├── pymatgen.analysis.diffusion.utils.supercells.rst.txt │ ├── pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.rst.txt │ ├── pymatgen.analysis.diffusion.utils.tests.test_maggma.rst.txt │ ├── pymatgen.analysis.diffusion.utils.tests.test_parse_entries.rst.txt │ ├── pymatgen.analysis.rst.txt │ ├── pymatgen.rst.txt │ ├── pymatgen_diffusion.aimd.rst.txt │ ├── pymatgen_diffusion.neb.rst.txt │ └── pymatgen_diffusion.rst.txt ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── ajax-loader.gif │ ├── basic.css │ ├── comment-bright.png │ ├── comment-close.png │ ├── comment.png │ ├── doctools.js │ ├── documentation_options.js │ ├── down-pressed.png │ ├── down.png │ ├── file.png │ ├── flasky.css │ ├── jquery-3.1.0.js │ ├── jquery-3.2.1.js │ ├── jquery-3.5.1.js │ ├── jquery-3.6.0.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── small_flask.css │ ├── sphinx_highlight.js │ ├── underscore-1.12.0.js │ ├── underscore-1.13.1.js │ ├── underscore-1.3.1.js │ ├── underscore.js │ ├── up-pressed.png │ ├── up.png │ └── websupport.js ├── _themes │ └── README.html ├── change_log.html ├── doctrees │ ├── _themes │ │ └── README.doctree │ ├── change_log.doctree │ ├── environment.pickle │ ├── index.doctree │ ├── modules.doctree │ ├── pymatgen.analysis.diffusion.aimd.clustering.doctree │ ├── pymatgen.analysis.diffusion.aimd.doctree │ ├── pymatgen.analysis.diffusion.aimd.pathway.doctree │ ├── pymatgen.analysis.diffusion.aimd.rdf.doctree │ ├── pymatgen.analysis.diffusion.aimd.tests.test_clustering.doctree │ ├── pymatgen.analysis.diffusion.aimd.tests.test_pathway.doctree │ ├── pymatgen.analysis.diffusion.aimd.tests.test_rdf.doctree │ ├── pymatgen.analysis.diffusion.aimd.tests.test_van_hove.doctree │ ├── pymatgen.analysis.diffusion.aimd.van_hove.doctree │ ├── pymatgen.analysis.diffusion.analyzer.doctree │ ├── pymatgen.analysis.diffusion.doctree │ ├── pymatgen.analysis.diffusion.neb.doctree │ ├── pymatgen.analysis.diffusion.neb.full_path_mapper.doctree │ ├── pymatgen.analysis.diffusion.neb.io.doctree │ ├── pymatgen.analysis.diffusion.neb.pathfinder.doctree │ ├── pymatgen.analysis.diffusion.neb.periodic_dijkstra.doctree │ ├── pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.doctree │ ├── pymatgen.analysis.diffusion.neb.tests.test_io.doctree │ ├── pymatgen.analysis.diffusion.neb.tests.test_pathfinder.doctree │ ├── pymatgen.analysis.diffusion.tests.test_analyzer.doctree │ ├── pymatgen.analysis.diffusion.tests.test_pathfinder.doctree │ ├── pymatgen.analysis.diffusion.utils.doctree │ ├── pymatgen.analysis.diffusion.utils.edge_data_from_sc.doctree │ ├── pymatgen.analysis.diffusion.utils.maggma.doctree │ ├── pymatgen.analysis.diffusion.utils.parse_entries.doctree │ ├── pymatgen.analysis.diffusion.utils.supercells.doctree │ ├── pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.doctree │ ├── pymatgen.analysis.diffusion.utils.tests.test_maggma.doctree │ ├── pymatgen.analysis.diffusion.utils.tests.test_parse_entries.doctree │ ├── pymatgen.analysis.doctree │ ├── pymatgen.doctree │ ├── pymatgen_diffusion.aimd.doctree │ ├── pymatgen_diffusion.doctree │ └── pymatgen_diffusion.neb.doctree ├── genindex.html ├── index.html ├── modules.html ├── objects.inv ├── py-modindex.html ├── pymatgen.analysis.diffusion.aimd.clustering.html ├── pymatgen.analysis.diffusion.aimd.html ├── pymatgen.analysis.diffusion.aimd.pathway.html ├── pymatgen.analysis.diffusion.aimd.rdf.html ├── pymatgen.analysis.diffusion.aimd.tests.test_clustering.html ├── pymatgen.analysis.diffusion.aimd.tests.test_pathway.html ├── pymatgen.analysis.diffusion.aimd.tests.test_rdf.html ├── pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html ├── pymatgen.analysis.diffusion.aimd.van_hove.html ├── pymatgen.analysis.diffusion.analyzer.html ├── pymatgen.analysis.diffusion.html ├── pymatgen.analysis.diffusion.neb.full_path_mapper.html ├── pymatgen.analysis.diffusion.neb.html ├── pymatgen.analysis.diffusion.neb.io.html ├── pymatgen.analysis.diffusion.neb.pathfinder.html ├── pymatgen.analysis.diffusion.neb.periodic_dijkstra.html ├── pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html ├── pymatgen.analysis.diffusion.neb.tests.test_io.html ├── pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html ├── pymatgen.analysis.diffusion.tests.test_analyzer.html ├── pymatgen.analysis.diffusion.tests.test_pathfinder.html ├── pymatgen.analysis.diffusion.utils.edge_data_from_sc.html ├── pymatgen.analysis.diffusion.utils.html ├── pymatgen.analysis.diffusion.utils.maggma.html ├── pymatgen.analysis.diffusion.utils.parse_entries.html ├── pymatgen.analysis.diffusion.utils.supercells.html ├── pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.html ├── pymatgen.analysis.diffusion.utils.tests.test_maggma.html ├── pymatgen.analysis.diffusion.utils.tests.test_parse_entries.html ├── pymatgen.analysis.html ├── pymatgen.html ├── pymatgen_diffusion.aimd.html ├── pymatgen_diffusion.html ├── pymatgen_diffusion.neb.html ├── search.html └── searchindex.js ├── docs_rst ├── Makefile ├── _templates │ └── layout.html ├── _themes │ ├── LICENSE │ ├── README.rst │ ├── flask_theme_support.py │ ├── kr │ │ ├── layout.html │ │ ├── relations.html │ │ ├── static │ │ │ ├── flasky.css_t │ │ │ └── small_flask.css │ │ └── theme.conf │ └── kr_small │ │ ├── layout.html │ │ ├── static │ │ └── flasky.css_t │ │ └── theme.conf ├── change_log.rst ├── conf.py ├── index.rst ├── make.bat ├── modules.rst ├── pymatgen.analysis.diffusion.aimd.clustering.rst ├── pymatgen.analysis.diffusion.aimd.pathway.rst ├── pymatgen.analysis.diffusion.aimd.rdf.rst ├── pymatgen.analysis.diffusion.aimd.rst ├── pymatgen.analysis.diffusion.aimd.tests.test_clustering.rst ├── pymatgen.analysis.diffusion.aimd.tests.test_pathway.rst ├── pymatgen.analysis.diffusion.aimd.tests.test_rdf.rst ├── pymatgen.analysis.diffusion.aimd.tests.test_van_hove.rst ├── pymatgen.analysis.diffusion.aimd.van_hove.rst ├── pymatgen.analysis.diffusion.analyzer.rst ├── pymatgen.analysis.diffusion.neb.full_path_mapper.rst ├── pymatgen.analysis.diffusion.neb.io.rst ├── pymatgen.analysis.diffusion.neb.pathfinder.rst ├── pymatgen.analysis.diffusion.neb.periodic_dijkstra.rst ├── pymatgen.analysis.diffusion.neb.rst ├── pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.rst ├── pymatgen.analysis.diffusion.neb.tests.test_io.rst ├── pymatgen.analysis.diffusion.neb.tests.test_pathfinder.rst ├── pymatgen.analysis.diffusion.rst ├── pymatgen.analysis.diffusion.tests.test_analyzer.rst ├── pymatgen.analysis.diffusion.tests.test_pathfinder.rst ├── pymatgen.analysis.diffusion.utils.edge_data_from_sc.rst ├── pymatgen.analysis.diffusion.utils.maggma.rst ├── pymatgen.analysis.diffusion.utils.parse_entries.rst ├── pymatgen.analysis.diffusion.utils.rst ├── pymatgen.analysis.diffusion.utils.supercells.rst ├── pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.rst ├── pymatgen.analysis.diffusion.utils.tests.test_maggma.rst ├── pymatgen.analysis.diffusion.utils.tests.test_parse_entries.rst ├── pymatgen.analysis.rst ├── pymatgen.rst ├── pymatgen_diffusion.aimd.rst ├── pymatgen_diffusion.neb.rst └── pymatgen_diffusion.rst ├── examples ├── CHGCAR_new.vasp ├── CHGCAR_new2.vasp ├── neb_idpp_solver.ipynb ├── neb_path_mapping.ipynb ├── probability_analysis.ipynb ├── radial_distribution_function.ipynb └── van_hove.ipynb ├── pyproject.toml ├── requirements-ci.txt ├── requirements.txt ├── src └── pymatgen │ └── analysis │ └── diffusion │ ├── __init__.py │ ├── aimd │ ├── __init__.py │ ├── clustering.py │ ├── pathway.py │ ├── rdf.py │ └── van_hove.py │ ├── analyzer.py │ ├── neb │ ├── __init__.py │ ├── full_path_mapper.py │ ├── io.py │ ├── pathfinder.py │ └── periodic_dijkstra.py │ └── utils │ ├── __init__.py │ ├── edge_data_from_sc.py │ ├── maggma.py │ ├── parse_entries.py │ └── supercells.py ├── tasks.py ├── tests └── pymatgen │ └── analysis │ └── diffusion │ ├── DiffusionAnalyzer.json │ ├── DiffusionAnalyzer_NPT.json │ ├── aimd │ ├── CHGCAR_new.vasp │ ├── __init__.py │ ├── cNa3PS4.cif │ ├── cNa3PS4_pda.json │ ├── cNa3PS4_trajectories.npy │ ├── test_clustering.py │ ├── test_pathway.py │ ├── test_rdf.py │ └── test_van_hove.py │ ├── migration_graph_spinel_MgMn2O4.json │ ├── neb │ ├── __init__.py │ ├── full_path_files │ │ ├── AECCAR_Mn6O5F7.vasp │ │ ├── Li6MnO4.cif │ │ ├── LixMn6O5F7_full_sites.json │ │ ├── Mg_2atom.vasp │ │ ├── Mn6O5F7_cat_migration.json │ │ ├── MnO2_full_Li.vasp │ │ └── li_ent.json │ ├── io_files │ │ ├── POSCAR │ │ ├── POSCAR0 │ │ ├── POSCAR1 │ │ ├── POSCAR2 │ │ ├── POSCAR_ep0 │ │ └── POSCAR_ep1 │ ├── pathfinder_files │ │ ├── CHGCAR.MnO2.vasp │ │ ├── CONTCAR-0 │ │ ├── CONTCAR-1 │ │ ├── LYPS.cif │ │ ├── Li6MnO4.json │ │ └── POSCAR.MnO2.all_sites.vasp │ ├── test_full_path_mapper.py │ ├── test_io.py │ └── test_pathfinder.py │ ├── test_analyzer.py │ ├── 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