{"id":46840962,"url":"https://github.com/zyumse/m2dtools","last_synced_at":"2026-03-10T13:04:39.869Z","repository":{"id":315107142,"uuid":"1058069189","full_name":"zyumse/m2dtools","owner":"zyumse","description":"tools for MD-based research projects","archived":false,"fork":false,"pushed_at":"2026-02-10T16:12:00.000Z","size":879,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-10T20:47:48.568Z","etag":null,"topics":["lammps","molecular-dynamics"],"latest_commit_sha":null,"homepage":"https://zyumse.github.io/m2dtools/","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/zyumse.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-16T15:23:45.000Z","updated_at":"2026-02-04T18:52:58.000Z","dependencies_parsed_at":"2025-09-16T19:58:25.678Z","dependency_job_id":"7679ebef-88ed-4888-890f-1f1498d1afec","html_url":"https://github.com/zyumse/m2dtools","commit_stats":null,"previous_names":["zyumse/md2tools","zyumse/m2dtools"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/zyumse/m2dtools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zyumse%2Fm2dtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zyumse%2Fm2dtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zyumse%2Fm2dtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zyumse%2Fm2dtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zyumse","download_url":"https://codeload.github.com/zyumse/m2dtools/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zyumse%2Fm2dtools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30334412,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-10T12:41:07.687Z","status":"ssl_error","status_checked_at":"2026-03-10T12:41:06.728Z","response_time":106,"last_error":"SSL_read: 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":["lammps","molecular-dynamics"],"created_at":"2026-03-10T13:04:39.245Z","updated_at":"2026-03-10T13:04:39.852Z","avatar_url":"https://github.com/zyumse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# m2dtools\n\n*m2dtools* is a lightweight Python toolkit for molecular simulation workflows, including analysis helpers, coarse-graining pipelines, and LAMMPS structure preparation scripts.\n\n📘 **Full Documentation:**  \nhttps://zyumse.github.io/m2dtools/\n\n## Installation\n\n   ```\n   pip install m2dtools\n   ```\n\n1. Clone this repository and move into it.\n2. (Optional) Create and activate a Python 3.8+ environment.\n3. Install the package in editable mode:\n\n   ```bash\n   pip install -e .\n   ```\n\nThis pulls in the core dependencies (`numpy`, `matplotlib`, `scipy`, `pandas`). Editable mode lets you modify the source and use the changes immediately without reinstalling.\n\n## Features\n\n- `m2dtools.basic` – vectorised analysis functions for bonds, angles, PDFs/SQs, coordination numbers, autocorrelation, MSD, and compressibility.\n- `m2dtools.lmp` – utilities to read, modify, and write LAMMPS full-data and dump files for simulation setup.\n- `m2dtools.cg` – coarse-graining tools, including iterative Boltzmann inversion (IBI) scripts and polymer-specific helpers.\n- `m2dtools.network` – routines for stochastic network generation and conversion to LAMMPS structures.\n- `m2dtools.other` – format converters and domain-specific helpers (e.g. GROMACS parsing, local stress extraction, silica and water coarse-graining utilities).\n\n## Contributing\n\nContributions are welcome.  \nPlease open an issue or submit a pull request on GitHub.\n\n## License\n\nReleased under the MIT License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzyumse%2Fm2dtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzyumse%2Fm2dtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzyumse%2Fm2dtools/lists"}