{"id":19528280,"url":"https://github.com/nomad-coe/nomad-parser-lammps","last_synced_at":"2026-03-01T09:33:15.397Z","repository":{"id":44632225,"uuid":"347107434","full_name":"nomad-coe/nomad-parser-lammps","owner":"nomad-coe","description":"This is a NOMAD parser for LAMMPS. It will read LAMMPS input and output files and provide all information in NOMAD's unified Metainfo based Archive format.","archived":false,"fork":false,"pushed_at":"2022-02-23T09:03:23.000Z","size":19008,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-26T02:31:57.305Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Roff","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nomad-coe.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-03-12T15:13:58.000Z","updated_at":"2021-05-21T01:30:46.000Z","dependencies_parsed_at":"2022-09-21T01:11:44.443Z","dependency_job_id":null,"html_url":"https://github.com/nomad-coe/nomad-parser-lammps","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/nomad-coe/nomad-parser-lammps","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nomad-coe%2Fnomad-parser-lammps","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nomad-coe%2Fnomad-parser-lammps/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nomad-coe%2Fnomad-parser-lammps/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nomad-coe%2Fnomad-parser-lammps/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nomad-coe","download_url":"https://codeload.github.com/nomad-coe/nomad-parser-lammps/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nomad-coe%2Fnomad-parser-lammps/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29965643,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-01T09:33:09.965Z","status":"ssl_error","status_checked_at":"2026-03-01T09:25:48.915Z","response_time":124,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2024-11-11T01:18:13.192Z","updated_at":"2026-03-01T09:33:15.372Z","avatar_url":"https://github.com/nomad-coe.png","language":"Roff","funding_links":[],"categories":[],"sub_categories":[],"readme":"This is a NOMAD parser for [LAMMPS](https://lammps.sandia.gov/). It will read LAMMPS input and\noutput files and provide all information in NOMAD's unified Metainfo based Archive format.\n\n## Preparing code input and output file for uploading to NOMAD\n\nNOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary\nfiles and directories. NOMAD will automatically try to choose the right parser for you files.\nFor each parser (i.e. for each supported code) there is one type of file that the respective\nparser can recognize. We call these files `mainfiles` as they typically are the main\noutput file a code. For each `mainfile` that NOMAD discovers it will create an entry\nin the database that users can search, view, and download. NOMAD will associate all files\nin the same directory as files that also belong to that entry. Parsers\nmight also read information from these auxillary files. This way you can add more files\nto an entry, even if the respective parser/code might not directly support it.\n\nFor LAMMPS please provide at least the files from this table if applicable to your\ncalculations (remember that you can provide more files if you want):\n\n\n\nTo create an upload with all calculations in a directory structure:\n\n```\nzip -r \u003cupload-file\u003e.zip \u003cdirectory\u003e/*\n```\n\nGo to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files\nor find instructions about how to upload files from the command line.\n\n## Using the parser\n\nYou can use NOMAD's parsers and normalizers locally on your computer. You need to install\nNOMAD's pypi package:\n\n```\npip install nomad-lab\n```\n\nTo parse code input/output from the command line, you can use NOMAD's command line\ninterface (CLI) and print the processing results output to stdout:\n\n```\nnomad parse --show-archive \u003cpath-to-file\u003e\n```\n\nTo parse a file in Python, you can program something like this:\n```python\nimport sys\nfrom nomad.cli.parse import parse, normalize_all\n\n# match and run the parser\narchive = parse(sys.argv[1])\n# run all normalizers\nnormalize_all(archive)\n\n# get the 'main section' section_run as a metainfo object\nsection_run = archive.section_run[0]\n\n# get the same data as JSON serializable Python dict\npython_dict = section_run.m_to_dict()\n```\n\n## Developing the parser\n\nCreate a virtual environment to install the parser in development mode:\n\n```\npip install virtualenv\nvirtualenv -p `which python3` .pyenv\nsource .pyenv/bin/activate\n```\n\nInstall NOMAD's pypi package:\n\n```\npip install nomad-lab\n```\n\nClone the parser project and install it in development mode:\n\n```\ngit clone https://github.com/nomad-coe/nomad-parser-lammps.git nomad-parser-lammps\npip install -e nomad-parser-lammps\n```\n\nRunning the parser now, will use the parser's Python code from the clone project.\n\n$parserSpecific$","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnomad-coe%2Fnomad-parser-lammps","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnomad-coe%2Fnomad-parser-lammps","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnomad-coe%2Fnomad-parser-lammps/lists"}