{"id":17255099,"url":"https://github.com/unixjunkie/vdw_grid_bench","last_synced_at":"2025-04-14T05:40:37.450Z","repository":{"id":223771452,"uuid":"761506453","full_name":"UnixJunkie/vdW_grid_bench","owner":"UnixJunkie","description":"Van der Waals 3D grid initialization benchmark","archived":false,"fork":false,"pushed_at":"2024-02-28T02:22:58.000Z","size":38,"stargazers_count":4,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-27T19:23:15.693Z","etag":null,"topics":["computational-chemistry","high-performance-computing","molecular-mechanics","ocaml-program","van-der-waals"],"latest_commit_sha":null,"homepage":"","language":"OCaml","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/UnixJunkie.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":"2024-02-22T00:34:55.000Z","updated_at":"2024-02-22T22:42:01.000Z","dependencies_parsed_at":"2024-02-26T05:41:29.242Z","dependency_job_id":null,"html_url":"https://github.com/UnixJunkie/vdW_grid_bench","commit_stats":null,"previous_names":["unixjunkie/vdw_grid_bench"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FvdW_grid_bench","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FvdW_grid_bench/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FvdW_grid_bench/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FvdW_grid_bench/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/vdW_grid_bench/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248830416,"owners_count":21168271,"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":["computational-chemistry","high-performance-computing","molecular-mechanics","ocaml-program","van-der-waals"],"created_at":"2024-10-15T07:10:42.238Z","updated_at":"2025-04-14T05:40:37.424Z","avatar_url":"https://github.com/UnixJunkie.png","language":"OCaml","readme":"# vdW_grid_bench\nVan der Waals 3D grid initialization benchmark\n\n# problem statement\nWe want to know the interaction energy between one\natom [l_a] located at any grid point [i,j,k] and a fixed set of atoms [A].\nWe use the Van der Waals non-bonded interaction energy and\nUniversal Force Field (UFF) parameters.\n\n# standard OCaml; before loop modification\ntime ./grid_init -dx 0.1 -l data/lig.pqrs -p data/prot.pqrs \nreal    1m19.899s\n\n# w/ dune's --profile=release\nreal    1m10.603s\n\n# w/ V3 @@inline annotations plus dist2 optims\nreal    0m57.384s\n\n# w/ optims in vdW_grid\nreal    0m49.096s\n\n# w/ pow3 and V3.dist2 instead of pow6 and V3.dist in vdW_grid\nreal    0m41.282s\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fvdw_grid_bench","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fvdw_grid_bench","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fvdw_grid_bench/lists"}