{"id":18525024,"url":"https://github.com/klarh/flowws-examples","last_synced_at":"2026-05-15T20:05:18.535Z","repository":{"id":75089320,"uuid":"240270559","full_name":"klarh/flowws-examples","owner":"klarh","description":"Example workflows using the flowws library","archived":false,"fork":false,"pushed_at":"2020-06-22T14:45:28.000Z","size":14,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-07-25T00:19:19.204Z","etag":null,"topics":["examples","molecular-dynamics","molecular-simulation","notebook","python","simulation","visualization","workflows"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/klarh.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}},"created_at":"2020-02-13T13:46:13.000Z","updated_at":"2020-06-22T14:45:30.000Z","dependencies_parsed_at":null,"dependency_job_id":"d564dbb4-5e53-42c6-abfe-843f290b78c5","html_url":"https://github.com/klarh/flowws-examples","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/klarh/flowws-examples","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/klarh%2Fflowws-examples","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/klarh%2Fflowws-examples/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/klarh%2Fflowws-examples/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/klarh%2Fflowws-examples/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/klarh","download_url":"https://codeload.github.com/klarh/flowws-examples/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/klarh%2Fflowws-examples/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33078026,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-15T11:35:32.926Z","status":"ssl_error","status_checked_at":"2026-05-15T11:35:31.362Z","response_time":103,"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":["examples","molecular-dynamics","molecular-simulation","notebook","python","simulation","visualization","workflows"],"created_at":"2024-11-06T17:44:13.691Z","updated_at":"2026-05-15T20:05:18.516Z","avatar_url":"https://github.com/klarh.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/klarh/flowws-examples/master)\n\n[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/klarh/flowws-examples/blob/master/)\n\n# Introduction\n\nThis repository demonstrates several workflows for simulation,\nvisualization, and analysis using\n[flowws](https://github.com/klarh/flowws).\n\nTo launch an interactive notebook server using mybinder.org, use the\nlink above; otherwise, install the prerequisites below to run\nlocally. Google colab is also supported somewhat, but see the caveats\nin the section below.\n\n# Prerequisites\n\nNote that not all of these are required for all notebooks. Everything\nexcept for hoomd is available on the PyPI and is available using `pip\ninstall -r requirements.txt`:\n\n- flowws\n- flowws-analysis\n- flowws-freud\n- freud-analysis\n- gtar\n- [hoomd-blue](https://hoomd-blue.readthedocs.io/en/stable/installation.html)\n- hoomd_flowws\n- matplotlib\n- plato-draw\n- pyriodic-aflow\n- pyside2\n- vispy (if using a notebook, make sure to follow the [installation instructions](http://vispy.org/installation.html))\n\n# Running on Google Colab\n\nExample notebooks can also run in [Google\nColab](https://colab.research.google.com), although it can be annoying\nto install prerequisites like HOOMD on a colab notebook. Note that\ninteractive plato backends are unlikely to work in colab. You can use\nthe following code in each notebook to install prerequisites:\n\n```\n!pip install -U -q PyDrive\n\n# download compiled hoomd release\nfrom pydrive.auth import GoogleAuth\nfrom pydrive.drive import GoogleDrive\nfrom google.colab import auth\nfrom oauth2client.client import GoogleCredentials\nauth.authenticate_user()\ngauth = GoogleAuth()\ngauth.credentials = GoogleCredentials.get_application_default()\ndrive = GoogleDrive(gauth)\nfileId = '1sbyj-ruKLtEK-9qVlsXSJU0hxCHf_blD'\ndownloaded = drive.CreateFile({'id': fileId})\ndownloaded.GetContentFile('hoomd.tar.gz')\n\n# extract hoomd\n!mkdir -p \"$(python -c 'import site;print(site.USER_SITE)')\"\n!tar xC \"$(python -c 'import site;print(site.USER_SITE)')\" -f hoomd.tar.gz\n\n# install other dependencies\n!apt-get install povray\n!pip install flowws-analysis flowws-freud freud-analysis gtar hoomd-flowws matplotlib plato-draw pyriodic-aflow\n\n# hoomd won't be able to be imported the first time this cell is run, so\n# restart the process.\ntry:\n    import hoomd\nexcept ImportError:\n    exit()\n```\n\n**Note:** The hoomd package is compiled with GPU support; select a GPU\nruntime (\"Runtime -\u003e Change runtime type\") to be able to correctly import it.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fklarh%2Fflowws-examples","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fklarh%2Fflowws-examples","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fklarh%2Fflowws-examples/lists"}