{"id":20296970,"url":"https://github.com/nbehrnd/clustergen_tools","last_synced_at":"2025-07-21T10:05:04.767Z","repository":{"id":154641914,"uuid":"201446100","full_name":"nbehrnd/clustergen_tools","owner":"nbehrnd","description":"Scripts to faciliate programmatic dimer and cluster generation with CLUSTERGEN","archived":false,"fork":false,"pushed_at":"2019-08-09T11:07:34.000Z","size":21,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-04T05:43:25.487Z","etag":null,"topics":["adf","cif","cluster","clustergen","clustering","crystallography","dimer","gaussian","python","xyz"],"latest_commit_sha":null,"homepage":"http://www.photocrystallography.eu/software.html","language":"Python","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/nbehrnd.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":"2019-08-09T10:27:27.000Z","updated_at":"2019-08-09T11:34:03.000Z","dependencies_parsed_at":null,"dependency_job_id":"7c3de28c-657f-4bf4-a5e2-54ea0c3f30a9","html_url":"https://github.com/nbehrnd/clustergen_tools","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nbehrnd/clustergen_tools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbehrnd%2Fclustergen_tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbehrnd%2Fclustergen_tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbehrnd%2Fclustergen_tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbehrnd%2Fclustergen_tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nbehrnd","download_url":"https://codeload.github.com/nbehrnd/clustergen_tools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nbehrnd%2Fclustergen_tools/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266278375,"owners_count":23904040,"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":["adf","cif","cluster","clustergen","clustering","crystallography","dimer","gaussian","python","xyz"],"created_at":"2024-11-14T15:42:27.274Z","updated_at":"2025-07-21T10:05:04.738Z","avatar_url":"https://github.com/nbehrnd.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Table of Contents\n\n1.  [Background](#org75902d7)\n2.  [Use](#org7a0f4fa)\n\n\n\u003ca id=\"org75902d7\"\u003e\u003c/a\u003e\n\n# Background\n\nBased on `.cif` files, CLUSTERGEN\u003csup\u003e\u003ca id=\"fnr.1\" class=\"footref\" href=\"#fn.1\"\u003e1\u003c/a\u003e\u003c/sup\u003e provides facilitates to\nidentify and write `.xyz` files about dimers and clusters suitable\nfor further analysis and quantum chemical computation.  It equally\noffers the direct output in formats suitable for ADF and Gaussian.\n\nTo automate the identification of \"interesting dimers\", `.cif` model\ndata may be converted batch-wise into intermediate `.inp` input files\nsuitable for a sequential processing with CLUSTERGEN's `.f90` source\ncode.  Similarly, it is possible to systematically build clusters.\nThree complementary definitions regarding the distance threshold of\ninner (reference) molecule and most outer neighbor are available.\n\n\n\u003ca id=\"org7a0f4fa\"\u003e\u003c/a\u003e\n\n# Use\n\nPut the `.cif` of interest, the `.f90` source code of CLUSTERGEN\n(available from the author) and the two scripts into the same\nfolder.  A call of\n\n    python cif2clustergen.py\n\ncreates the intermediate `.inp` files.  A subsequent\n\n    python serial_clustergen.py\n\nthen both compiles the source-code with `gfortran`, as well provides\nthe results accessed by `CLUSTERGEN`.\n\n\n# Footnotes\n\n\u003csup\u003e\u003ca id=\"fn.1\" href=\"#fnr.1\"\u003e1\u003c/a\u003e\u003c/sup\u003e \"CLUSTERGEN: a program for molecular cluster generation from\ncrystallographic data\", R. Kaminski, K. N. Jarzembska and S. Domagala\nin *J. Appl. Cryst.* (2013) ****46****, 540-543,\n[doi:10.1107/S0021889813002173](10.1107/S0021889813002173); Windows compiled executable on\n[http://www.photocrystallography.eu/software.html](http://www.photocrystallography.eu/software.html).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbehrnd%2Fclustergen_tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnbehrnd%2Fclustergen_tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbehrnd%2Fclustergen_tools/lists"}