{"id":31835079,"url":"https://github.com/matthewghgriffiths/fastoverlap","last_synced_at":"2026-03-05T07:36:25.071Z","repository":{"id":201537731,"uuid":"82290873","full_name":"matthewghgriffiths/fastoverlap","owner":"matthewghgriffiths","description":"Algorithms for fast alignment of structures in finite and periodic systems.","archived":false,"fork":false,"pushed_at":"2022-08-11T15:09:49.000Z","size":7829,"stargazers_count":10,"open_issues_count":3,"forks_count":6,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-10-19T21:41:59.187Z","etag":null,"topics":["alignment","energy-landscapes","numpy","python","special-orthogonal-group-transforms"],"latest_commit_sha":null,"homepage":null,"language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/matthewghgriffiths.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}},"created_at":"2017-02-17T11:28:32.000Z","updated_at":"2023-10-19T23:19:31.670Z","dependencies_parsed_at":null,"dependency_job_id":"5ce0eaa0-6cbd-4ae3-b024-b37a8f71f5af","html_url":"https://github.com/matthewghgriffiths/fastoverlap","commit_stats":null,"previous_names":["matthewghgriffiths/fastoverlap"],"tags_count":null,"template":null,"template_full_name":null,"purl":"pkg:github/matthewghgriffiths/fastoverlap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewghgriffiths%2Ffastoverlap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewghgriffiths%2Ffastoverlap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewghgriffiths%2Ffastoverlap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewghgriffiths%2Ffastoverlap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/matthewghgriffiths","download_url":"https://codeload.github.com/matthewghgriffiths/fastoverlap/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthewghgriffiths%2Ffastoverlap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279009508,"owners_count":26084609,"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","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["alignment","energy-landscapes","numpy","python","special-orthogonal-group-transforms"],"created_at":"2025-10-12T00:55:57.047Z","updated_at":"2025-10-12T00:55:58.050Z","avatar_url":"https://github.com/matthewghgriffiths.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FASTOVERLAP\nAlgorithms for fast alignment of structures in finite and periodic systems. These methods are also implemented in the [Cambridge Energy Landscape Software](http://www-wales.ch.cam.ac.uk/software.html) in `GMIN` and `OPTIM`.\n\nFASTOVERLAP can be run 'as is' with no compilation required using `PeriodicAlign` and `SphericalAlign`. The Fortran modules need to be compiled to peform branch and bound alignments with `BranchnBoundAlignment`. \n\nThese algorithms have been detailed in the paper,\n\n**Optimal Alignment of Structures for Finite and Periodic Systems** Matthew Griffiths, Samuel P. Niblett, and David J. Wales _Journal of Chemical\nTheory and Computation_ **2017** 13(10), 4914-4931, doi:[10.1021/acs.jctc.7b00543](http://dx.doi.org/10.1021/acs.jctc.7b00543)\n\nIf you use this module, please cite the above paper.\n\n![Difference between FASTOVERLAP (maximising overlap) vs Branch and Bound Alignment (minimising RMSD)](./alignment.gif)\n\n## INSTALLATION\n\n## Required packages\n\n### python packages:\n\n1. `numpy`:\n  We use numpy everywhere for doing numerical work. It also installs `f2py` which is used to compile fortran code into modules callable by python.\n\n2. `scipy`:\n  For some of the optimizers and various scientific tools\n\n3. [`munkres`](https://pypi.org/project/munkres/) or [`pele`](http://pele-python.github.io/pele/):\n  To solve the linear assignment problem for permutational alignment.\n\n### for compilation:\n\n1. Fortran compiler\n2. `fftw`\n3. `lapack`\n\n## Compilation\n\nThe modules can be compiled using `numpy.distutils` to build the Fortran Modules in place\n\n```\n$ python setup.py build_ext -i\n```\n\nalternative the `f2py` modules can be directly compiled by running\n\n```\n$ ./compile.sh\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthewghgriffiths%2Ffastoverlap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatthewghgriffiths%2Ffastoverlap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthewghgriffiths%2Ffastoverlap/lists"}