{"id":16519108,"url":"https://github.com/pdebuyl/pyh5md","last_synced_at":"2025-10-28T07:31:23.354Z","repository":{"id":6126022,"uuid":"7354249","full_name":"pdebuyl/pyh5md","owner":"pdebuyl","description":"Read and write H5MD files","archived":false,"fork":false,"pushed_at":"2017-12-19T15:21:57.000Z","size":95,"stargazers_count":12,"open_issues_count":1,"forks_count":5,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-01T12:45:27.822Z","etag":null,"topics":["hdf5","molecular-dynamics"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pdebuyl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2012-12-28T12:45:13.000Z","updated_at":"2024-07-10T07:18:42.000Z","dependencies_parsed_at":"2022-09-13T21:50:48.726Z","dependency_job_id":null,"html_url":"https://github.com/pdebuyl/pyh5md","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/pdebuyl%2Fpyh5md","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdebuyl%2Fpyh5md/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdebuyl%2Fpyh5md/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdebuyl%2Fpyh5md/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdebuyl","download_url":"https://codeload.github.com/pdebuyl/pyh5md/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238614487,"owners_count":19501470,"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":["hdf5","molecular-dynamics"],"created_at":"2024-10-11T16:45:13.829Z","updated_at":"2025-10-28T07:31:23.349Z","avatar_url":"https://github.com/pdebuyl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"pyh5md : Read and write H5MD files\n==================================\n\nCopyright 2012-2017,2025 Pierre de Buyl and contributors  \n*License:* BSD\n\npyh5md is a library to read and write easily H5MD files. [H5MD][] is a file\nformat specification based on [HDF5][] to store molecular data. pyh5md is built\non top of [h5py][], the HDF5 for Python library by Andrew Colette.\n\n[H5MD]: http://nongnu.org/h5md/\n[HDF5]: http://www.hdfgroup.org/HDF5/\n[h5py]: http://h5py.org/\n\npyh5md used to define a complex class structure. Since version 1.0.0.dev1, a light\nsubclassing of h5py's classes is used instead.\n\nInstall\n-------\n\nIt is recommended to install in a virtual environment. Then,\n\n    pip install pyh5md\n\ninstalls pyh5md in that virtual environment. To install from the git repository:\n\n    pip install .\n\nExamples\n--------\n\nOnce pyh5md is installed:\n\n    cd examples\n    python random_walk_1d.py\n\nexecutes an example program that generates the H5MD file `walk_1d.h5`.\n\nUsage\n-----\n\nTo write data to a particles group named \"atoms\", with a fixed set of positions:\n\n```\nfrom pyh5md import File, element\nkwargs = {'creator': 'pyh5md README example',\n\t      'author': 'Pierre de Buyl',\n          }\nwith File('new_file.h5', 'w', **kwargs) as f:\n    g = f.particles_group('atoms')\n    g.create_box(dimension=3, boundary=['none']*3)\n    element(g, 'position', store='fixed', data=np.random.random(size=(32, 3)))\n```\n\nTo read data from a H5MD file created with, for instance, LAMMPS:\n\n```\nfrom pyh5md import File, element\nwith File('dump_3d.h5', 'r') as f:\n    g = f.particles_group('all')\n    box_edges = element(g, 'box/edges').value[0]\n    position = element(g, 'position').value[:]\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdebuyl%2Fpyh5md","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdebuyl%2Fpyh5md","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdebuyl%2Fpyh5md/lists"}