{"id":21140915,"url":"https://github.com/glotzerlab/hoomd-blue","last_synced_at":"2025-05-15T04:07:40.250Z","repository":{"id":37791987,"uuid":"147663007","full_name":"glotzerlab/hoomd-blue","owner":"glotzerlab","description":"Molecular dynamics and Monte Carlo soft matter simulation on GPUs.","archived":false,"fork":false,"pushed_at":"2025-05-08T14:59:28.000Z","size":75458,"stargazers_count":373,"open_issues_count":14,"forks_count":141,"subscribers_count":23,"default_branch":"trunk-patch","last_synced_at":"2025-05-08T15:31:44.310Z","etag":null,"topics":["conda-forge","cuda","docker","gpu","hard-particle","hoomd-blue","molecular-dynamics","monte-carlo-simulation","particle-system","python","simulation","singularity"],"latest_commit_sha":null,"homepage":"http://glotzerlab.engin.umich.edu/hoomd-blue","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/glotzerlab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.rst","contributing":"CONTRIBUTING.rst","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}},"created_at":"2018-09-06T11:23:27.000Z","updated_at":"2025-05-08T14:59:37.000Z","dependencies_parsed_at":"2022-06-22T16:23:12.153Z","dependency_job_id":"ee7c1e60-f6a1-4dd2-9704-55cc74fc86b3","html_url":"https://github.com/glotzerlab/hoomd-blue","commit_stats":null,"previous_names":[],"tags_count":126,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glotzerlab%2Fhoomd-blue","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glotzerlab%2Fhoomd-blue/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glotzerlab%2Fhoomd-blue/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/glotzerlab%2Fhoomd-blue/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/glotzerlab","download_url":"https://codeload.github.com/glotzerlab/hoomd-blue/tar.gz/refs/heads/trunk-patch","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254270646,"owners_count":22042859,"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":["conda-forge","cuda","docker","gpu","hard-particle","hoomd-blue","molecular-dynamics","monte-carlo-simulation","particle-system","python","simulation","singularity"],"created_at":"2024-11-20T07:18:50.790Z","updated_at":"2025-05-15T04:07:35.230Z","avatar_url":"https://github.com/glotzerlab.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![HOOMD-blue](sphinx-doc/hoomdblue-logo-horizontal.svg)](https://glotzerlab.engin.umich.edu/hoomd-blue/)\n\n[![Citing HOOMD](https://img.shields.io/badge/cite-hoomd-blue.svg)](https://hoomd-blue.readthedocs.io/en/latest/citing.html)\n[![conda-forge](https://img.shields.io/conda/vn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd)\n[![conda-forge Downloads](https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd)\n[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows//test.yaml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml)\n[![Read the Docs](https://img.shields.io/readthedocs/hoomd-blue/latest.svg)](https://hoomd-blue.readthedocs.io/en/latest/?badge=latest)\n[![Contributors](https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat)](https://hoomd-blue.readthedocs.io/en/latest/credits.html)\n[![License](https://img.shields.io/badge/license-BSD--3--Clause-green.svg)](LICENSE)\n\n**HOOMD-blue** is a Python package that runs simulations of particle systems on CPUs and GPUs. It\nperforms hard particle Monte Carlo simulations of a variety of shape classes and molecular dynamics\nsimulations of particles with a range of pair, bond, angle, and other potentials. Many features are\ntargeted at the soft matter research community, though the code is general and capable of many\ntypes of particle simulations.\n\n## Resources\n\n- [Documentation](https://hoomd-blue.readthedocs.io/):\n  Tutorial, full Python API description, and usage information.\n- [Citing HOOMD-blue](https://hoomd-blue.readthedocs.io/en/latest/citing.html)\n  How to cite the code.\n- [Installation guide](INSTALLING.rst):\n  Instructions for installing **HOOMD-blue** binaries.\n- [Compilation guide](BUILDING.rst):\n  Instructions for compiling **HOOMD-blue**.\n- [HOOMD-blue discussion board](https://github.com/glotzerlab/hoomd-blue/discussions/):\n  Ask the **HOOMD-blue** user community for help.\n- [HOOMD-blue website](https://glotzerlab.engin.umich.edu/hoomd-blue/):\n  Additional information and publications.\n- [HOOMD-blue benchmark scripts](https://github.com/glotzerlab/hoomd-benchmarks):\n  Scripts to evaluate the performance of HOOMD-blue simulations.\n- [HOOMD-blue validation tests](https://github.com/glotzerlab/hoomd-validation):\n  Scripts to validate that HOOMD-blue performs accurate simulations.\n\n## Related tools\n\n- [freud](https://freud.readthedocs.io/):\n  Analyze HOOMD-blue simulation results with the **freud** Python library.\n- [signac](https://signac.readthedocs.io/):\n  Manage your workflow with **signac**.\n\n## Example scripts\n\nThese examples demonstrate some of the Python API.\n\nHard particle Monte Carlo:\n```python\nimport hoomd\n\nmc = hoomd.hpmc.integrate.ConvexPolyhedron()\nmc.shape['octahedron'] = dict(vertices=[\n    (-0.5, 0, 0),\n    (0.5, 0, 0),\n    (0, -0.5, 0),\n    (0, 0.5, 0),\n    (0, 0, -0.5),\n    (0, 0, 0.5),\n])\n\ncpu = hoomd.device.CPU()\nsim = hoomd.Simulation(device=cpu, seed=20)\nsim.operations.integrator = mc\n# The tutorial describes how to construct an initial configuration 'init.gsd'.\nsim.create_state_from_gsd(filename='init.gsd')\n\nsim.run(1e5)\n```\n\nMolecular dynamics:\n```python\nimport hoomd\n\ncell = hoomd.md.nlist.Cell(buffer=0.4)\nlj = hoomd.md.pair.LJ(nlist=cell)\nlj.params[('A', 'A')] = dict(epsilon=1, sigma=1)\nlj.r_cut[('A', 'A')] = 2.5\n\nintegrator = hoomd.md.Integrator(dt=0.005)\nintegrator.forces.append(lj)\nbussi = hoomd.md.methods.thermostats.Bussi(kT=1.5)\nnvt = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All(), thermostat=bussi)\nintegrator.methods.append(nvt)\n\ngpu = hoomd.device.GPU()\nsim = hoomd.Simulation(device=gpu)\nsim.operations.integrator = integrator\n# The tutorial describes how to construct an initial configuration 'init.gsd'.\nsim.create_state_from_gsd(filename='init.gsd')\nsim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.5)\n\nsim.run(1e5)\n```\n\n## Change log\n\n[CHANGELOG.rst](CHANGELOG.rst) contains the full change log.\n\n## Contributing to HOOMD-blue\n\nContributions are welcomed via [pull requests](https://github.com/glotzerlab/hoomd-blue/pulls).\nPlease report bugs and suggest feature enhancements via the [issue\ntracker](https://github.com/glotzerlab/hoomd-blue/issues). See [CONTRIBUTING.rst](CONTRIBUTING.rst)\nand [ARCHITECTURE.md](ARCHITECTURE.md) for more information.\n\n## License\n\n**HOOMD-blue** is available under the [3-clause BSD license](LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fglotzerlab%2Fhoomd-blue","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fglotzerlab%2Fhoomd-blue","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fglotzerlab%2Fhoomd-blue/lists"}