{"id":15048470,"url":"https://github.com/snapex2409/komd","last_synced_at":"2026-01-02T13:06:50.228Z","repository":{"id":251662591,"uuid":"838064533","full_name":"Snapex2409/KoMD","owner":"Snapex2409","description":"Small MD framework","archived":false,"fork":false,"pushed_at":"2024-12-22T19:20:29.000Z","size":4444,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-13T23:13:54.480Z","etag":null,"topics":["kokkos","md","molecular-dynamics","simulation"],"latest_commit_sha":null,"homepage":"","language":"C++","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/Snapex2409.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":"2024-08-04T20:46:24.000Z","updated_at":"2024-12-22T19:20:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"90ad4abf-5738-47df-bcfe-21475c68820e","html_url":"https://github.com/Snapex2409/KoMD","commit_stats":null,"previous_names":["snapex2409/komd"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snapex2409%2FKoMD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snapex2409%2FKoMD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snapex2409%2FKoMD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snapex2409%2FKoMD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Snapex2409","download_url":"https://codeload.github.com/Snapex2409/KoMD/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243495495,"owners_count":20299923,"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":["kokkos","md","molecular-dynamics","simulation"],"created_at":"2024-09-24T21:13:19.943Z","updated_at":"2026-01-02T13:06:50.222Z","avatar_url":"https://github.com/Snapex2409.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# KoMD\nSmall MD framework\n\n\nThe intention is to provide a full MD framework for non-rigid multi-site molecular models. \nPortability is provided by using Kokkos. Currently, OpenMP and Cuda backends are supported.\n\n## Prequisites\n* vtk Library: ```sudo apt install libvtk\u003cversion\u003e-qt-dev``` minimum version: 7\n* For CUDA support: Install CUDA Toolkit, follow the instructions on the official CUDA Toolkit page.\n* For OpenMP support: Install OpenMP lib and runtime\n\n## Compilation\n* Create build directory ``` mkdir build \u0026\u0026 cd build``` \n* Configure CMake ``` cmake .. \u003coptions\u003e``` or ```ccmake ..```\n* CMake options:\n  * ENABLE_VTK:BOOL=ON|OFF\n  * CUDA options:\n    * CUDA_TOOLKIT_ROOT_DIR:FILEPATH=```\u003cpath to cuda installation\u003e```\n    * CUDAToolkit_INCLUDE_DIRECTORIES:FILEPATH=```\u003cpath to cuda installation\u003e/targets/x86_64-linux/include```\n    * CUDA_CUDART:FILEPATH=```\u003cpath to cuda installation\u003e/targets/x86_64-linux/lib```\n  * Kokkos options:\n    * Kokkos_ENABLE_```\u003cbackend\u003e```:BOOL=ON backend options are CUDA and OpenMP\n    * Kokkos_ARCH_NATIVE:BOOL=ON\n    * Kokkos_NVCC_WRAPPER:FILEPATH=```\u003cpath to KoMD repo\u003e```/dependencies-external/kokkos-4.3.01/bin/nvcc_wrapper\n    * Kokkos_ARCH_```\u003carch\u003e```:BOOL=ON set arch to used GPU architecture\n* Compile with ```make all```\n\n## Troubleshooting\n* When installing CUDA Toolkit, make sure it is fully installed and sourced. If it is not, then many CUDA tools and libs need to be symlinked into PATH directories.\n* Recommendation: Use ccmake to configure CMake. There all options will be visible.\n\n## Input File format\n* see ```examples/inp.dat```\n\n## Running KoMD\n* ```KoMD \u003cpath to input file\u003e```\n* When running with OpenMP, set these env variables: OMP_PROC_BIND=spread;OMP_NUM_THREADS=8\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnapex2409%2Fkomd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnapex2409%2Fkomd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnapex2409%2Fkomd/lists"}