{"id":16402309,"url":"https://github.com/linux-cpp-lisp/sitator","last_synced_at":"2025-08-01T07:31:24.555Z","repository":{"id":83704604,"uuid":"143292255","full_name":"Linux-cpp-lisp/sitator","owner":"Linux-cpp-lisp","description":"Unsupervised landmark analysis for jump detection in molecular dynamics simulations.","archived":false,"fork":false,"pushed_at":"2021-01-12T20:08:50.000Z","size":1836,"stargazers_count":13,"open_issues_count":1,"forks_count":6,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-04T13:07:39.033Z","etag":null,"topics":["materials-science","molecular-dynamics","site-analysis","solid-state-physics"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1103/PhysRevMaterials.3.055404","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Linux-cpp-lisp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-08-02T12:33:40.000Z","updated_at":"2025-03-16T20:50:01.000Z","dependencies_parsed_at":null,"dependency_job_id":"95182341-1670-41c0-9fed-8664adfcb65e","html_url":"https://github.com/Linux-cpp-lisp/sitator","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/Linux-cpp-lisp/sitator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Linux-cpp-lisp%2Fsitator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Linux-cpp-lisp%2Fsitator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Linux-cpp-lisp%2Fsitator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Linux-cpp-lisp%2Fsitator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Linux-cpp-lisp","download_url":"https://codeload.github.com/Linux-cpp-lisp/sitator/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Linux-cpp-lisp%2Fsitator/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268185559,"owners_count":24209392,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-01T02:00:08.611Z","response_time":67,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["materials-science","molecular-dynamics","site-analysis","solid-state-physics"],"created_at":"2024-10-11T05:45:49.729Z","updated_at":"2025-08-01T07:31:24.185Z","avatar_url":"https://github.com/Linux-cpp-lisp.png","language":"Python","readme":"# sitator\n\nA modular framework for conducting and visualizing site analysis of molecular dynamics trajectories.\n\n![](example.png)\n\n\u003ci\u003e Visualizations of complete landmark site analyses, created with `sitator`, of the superionic conductors (a) LGPS, (b) LLZO, and (c) LASO. Source: figures 11, 14, and 18 from our paper, linked below. \u003c/i\u003e\n\n\n`sitator` contains an efficient implementation of our method, landmark analysis, as well as visualization tools, generic data structures for site analysis, pre- and post-processing tools, and more.\n\nFor details on landmark analysis and its application, please see our paper:\n\n\u003e L. Kahle, A. Musaelian, N. Marzari, and B. Kozinsky \u003cbr/\u003e\n\u003e [Unsupervised landmark analysis for jump detection in molecular dynamics simulations](https://doi.org/10.1103/PhysRevMaterials.3.055404) \u003cbr/\u003e\n\u003e Phys. Rev. Materials 3, 055404 – 21 May 2019\n\nIf you use `sitator` in your research, please consider citing this paper. The BibTeX citation can be found in [`CITATION.bib`](CITATION.bib).\n\n## Installation\n\n`sitator` is built for Python \u003e=3.2 (the older version, v1.0.1, supports Python 2.7). We recommend the use of a virtual environment (`virtualenv`, `conda`, etc.). `sitator` has a number of optional dependencies that enable various features:\n\n\n* Landmark Analysis\n * The `network` executable from [Zeo++](http://www.maciejharanczyk.info/Zeopp/examples.html) is required for computing the Voronoi decomposition. (It does not have to be installed in `PATH`; the path to it can be given with the `zeopp_path` option of `VoronoiSiteGenerator`.)\n* Site Type Analysis\n * For SOAP-based site types: either the `quip` binary from [QUIP](https://libatoms.github.io/QUIP/) with [GAP](http://www.libatoms.org/gap/gap_download.html) **or** the [`DScribe`](https://singroup.github.io/dscribe/index.html) Python library.\n    * The Python 2.7 bindings for QUIP (`quippy`) are **not** required. Generally, `DScribe` is much simpler to install than QUIP. **Please note**, however, that the SOAP descriptor vectors **differ** between QUIP and `DScribe` and one or the other may give better results depending on the system you are analyzing.\n * For coordination environment analysis (`sitator.site_descriptors.SiteCoordinationEnvironment`), we integrate the `pymatgen.analysis.chemenv` package; a somewhat recent installation of `pymatgen` is required.\n\nAfter downloading, the package is installed with `pip`:\n\n```bash\n# git clone ... OR unzip ... OR ...\ncd sitator\npip install .\n```\n\nTo enable site type analysis, add the `[SiteTypeAnalysis]` option (this adds two dependencies -- Python packages `pydpc` and `dscribe`):\n\n```bash\npip install \".[SiteTypeAnalysis]\"\n```\n\n## Examples and Documentation\n\nTwo example Jupyter notebooks for conducting full landmark analyses of LiAlSiO\u003csub\u003e4\u003c/sub\u003e and Li\u003csub\u003e12\u003c/sub\u003eLa\u003csub\u003e3\u003c/sub\u003eZr\u003csub\u003e2\u003c/sub\u003eO\u003csub\u003e12\u003c/sub\u003e as in our paper, including data files, can be found [on Materials Cloud](https://archive.materialscloud.org/record/102).\n\nFull API documentation can be found at [ReadTheDocs](https://sitator.readthedocs.io/en/py3/).\n\n`sitator` generally assumes units of femtoseconds for time, Angstroms for space,\nand Cartesian (not crystal) coordinates.\n\n## Global Options\n\n`sitator` uses the `tqdm.autonotebook` tool to automatically produce the correct fancy progress bars for terminals and iPython notebooks. To disable all progress bars, run with the environment variable `SITATOR_PROGRESSBAR` set to `false`.\n\nThe `SITATOR_ZEO_PATH` and `SITATOR_QUIP_PATH` environment variables can set the default paths to the Zeo++ `network` and QUIP `quip` executables, respectively.\n\n## License\n\nThis software is made available under the MIT License. See [`LICENSE`](LICENSE) for more details.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinux-cpp-lisp%2Fsitator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinux-cpp-lisp%2Fsitator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinux-cpp-lisp%2Fsitator/lists"}