{"id":24030061,"url":"https://github.com/andeplane/atomify","last_synced_at":"2025-04-18T22:11:40.928Z","repository":{"id":61194674,"uuid":"361413203","full_name":"andeplane/atomify","owner":"andeplane","description":"Real time molecular dynamics in the browser using LAMMPS","archived":false,"fork":false,"pushed_at":"2024-11-16T20:41:20.000Z","size":256214,"stargazers_count":51,"open_issues_count":45,"forks_count":6,"subscribers_count":4,"default_branch":"main","last_synced_at":"2024-11-16T21:27:27.030Z","etag":null,"topics":["atomistic-simulations","lammps","molecular-dynamics","molecular-dynamics-simulation","molecular-simulation","visualization","webassembly","webgl"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/andeplane.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":".github/FUNDING.yml","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},"funding":{"github":["andeplane"]}},"created_at":"2021-04-25T11:45:35.000Z","updated_at":"2024-11-16T20:39:56.000Z","dependencies_parsed_at":"2024-11-05T10:52:09.332Z","dependency_job_id":null,"html_url":"https://github.com/andeplane/atomify","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andeplane%2Fatomify","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andeplane%2Fatomify/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andeplane%2Fatomify/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andeplane%2Fatomify/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andeplane","download_url":"https://codeload.github.com/andeplane/atomify/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":233067013,"owners_count":18620043,"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","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":["atomistic-simulations","lammps","molecular-dynamics","molecular-dynamics-simulation","molecular-simulation","visualization","webassembly","webgl"],"created_at":"2025-01-08T17:05:44.507Z","updated_at":"2025-01-08T17:10:03.404Z","avatar_url":"https://github.com/andeplane.png","language":"C++","funding_links":["https://github.com/sponsors/andeplane"],"categories":[],"sub_categories":[],"readme":"# Atomify - real time molecular dynamics simulations in the browser\n\n[![Deploy](https://github.com/andeplane/atomify/actions/workflows/deploy.yaml/badge.svg?branch=main)](https://github.com/andeplane/atomify/actions/workflows/deploy.yaml)\n\nTL;DR:\n\n- Run molecular dynamics (LAMMPS) in the browser\n- Upload your own scripts or run one of the built-in examples\n- Watch the simulation while it happens and view plots of real time physical quantities such as temperature and pressure\n- Analyze the simulation in a Jupyter notebook\n\n## ⚛️ Try it in your browser ⚛️\n\n➡️ **https://andeplane.github.io/atomify**\n\n➡️ **[Customize Atomify with your own simulations for e.g. teaching](https://github.com/andeplane/atomify-examples-template)** (this only takes a few minutes if you have simulations).\n\nTo see the latest changes, please check the [change log](CHANGELOG.md).\n\n![Atomify](atomify.gif)\n\nThe typical workflow when developing scripts for LAMMPS includes working with several programs. A text editor is needed to modify the scripts, the terminal to run LAMMPS, and programs like VMD or Ovito reading trajectories from a file dumped to the disk to visualize the system over time. If physical quantities are computed with LAMMPS, the data is often plotted with MATLAB or Python. This is a tedious process, especially for teaching purposes and for people who are new to LAMMPS.\n\nWe here introduce Atomify, a web editor running LAMMPS with real time visualization with stunning graphics, access to real time plotting of physical quantities and much more. After a simulation is finished, all files are available in a jupyter notebook that also runs in the browser.\n\n## How does it work?\n\nLAMMPS is compiled to [Webassembly](https://webassembly.org/) using [Emscripten](https://emscripten.org/) so it can run in the browser. It runs with about 50% of the speed of natively compiled LAMMPS (single threaded). The visualization is built on top of [three.js](https://threejs.org/), with specialized high performance rendering of spheres and cylinders. The Jupyter notebook is [Jupyterlite](https://jupyterlite.readthedocs.io/), and uses [Pyodide](https://pyodide.org/en/stable/), a Python runtime running entirely in the browser.\n\n## Customize example simulations\n\nYou can use this [Github template](https://github.com/andeplane/atomify-examples-template) to create your own set of simulations and Jupyter notebook analysis using Atomify. This does not require your own build or deployment of Atomify.\n\n## How to build and run locally\n\n### Prerequisites\n\n- [NodeJS](https://nodejs.org/en/) to install packages and run locally\n- [Emscripten](https://emscripten.org/) to compile LAMMPS to webassembly (optional)\n- [Python](https://www.python.org/) to run build script (optional)\n\n### Run locally\n\nClone the repository\n\n`git clone https://github.com/andeplane/atomify`\n\nInstall packages with NPM\n\n`npm install`\n\n### Compile LAMMPS (Optional: if you don't need to modify LAMMPS installation)\n\nEnsure that `em++` is in your path.\n\n```\ncd cpp\npython build.py\ncd ..\n```\n\n### Install JupyterLite (Optional: if you need Jupyter notebooks when running locally)\n\nCreate an empty Python environment (Python 3.12 is recommended)\nInstall packages\n\n```\npip install -r jupyterlite/requirements.txt\n```\n\nBuild JupyterLite\n\n```\njupyter lite build --contents jupyterlite/content --output-dir public/jupyter\n```\n\n### Run locally\n\n`npm run start`\nand open http://localhost:3000/atomify/ (remember the slash at the end)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandeplane%2Fatomify","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandeplane%2Fatomify","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandeplane%2Fatomify/lists"}