{"id":15904300,"url":"https://github.com/xiaohanzhangcmu/axiom","last_synced_at":"2025-10-05T15:24:01.656Z","repository":{"id":102485199,"uuid":"137242747","full_name":"XiaohanZhangCMU/axiom","owner":"XiaohanZhangCMU","description":"scalable C++ and python binding framework for Scientific Computing and Machine Learning","archived":false,"fork":false,"pushed_at":"2020-07-06T04:18:33.000Z","size":3844,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-08T11:15:12.636Z","etag":null,"topics":["deepq-learning","finite-element-methods","molecular-dynamics","stanford","tensorflow"],"latest_commit_sha":null,"homepage":"","language":"HTML","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/XiaohanZhangCMU.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-06-13T16:34:15.000Z","updated_at":"2020-07-06T04:18:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"33e90acb-5b6d-462f-9530-77a8661d2c61","html_url":"https://github.com/XiaohanZhangCMU/axiom","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/XiaohanZhangCMU%2Faxiom","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/XiaohanZhangCMU%2Faxiom/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/XiaohanZhangCMU%2Faxiom/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/XiaohanZhangCMU%2Faxiom/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/XiaohanZhangCMU","download_url":"https://codeload.github.com/XiaohanZhangCMU/axiom/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246892364,"owners_count":20850840,"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":["deepq-learning","finite-element-methods","molecular-dynamics","stanford","tensorflow"],"created_at":"2024-10-06T12:23:07.110Z","updated_at":"2025-10-05T15:24:01.599Z","avatar_url":"https://github.com/XiaohanZhangCMU.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Axiom Drives Scientific Computing Codes with Python\n\nAuthors: **aXioM**=**Xiao**Han+**Mo**Han :)\n\nThis framework helps bind (GPU/MPI-accelerated) C++ codes with Python using pybind11. For example, packages/mdsw implements Molecular Dynamics in C++ and it interfaces with OpenAI/gym environment through Python. New package can be added by following the existing examples. Axiom allows C++ and Python to communicate efficiently within memory through Numpy. Below shows an calculation done with mdsw -- the greedy search part is written in Python.\n\n\u003cfigcaption\u003e Minimum Atomistic Defect (Frank-Partial Dislocation) Nucleation Energy Barrier Found by Greedy Algorithm \u003c/figcaption\u003e\n\u003cimg src=\"animation.gif\" alt=\"Drawing\" style=\"width: 400px;\"/\u003e\n\n\n## Installation requirement:\n1) OS X \u003e Yosemite, Linux: CentOS \u003e= 7.5.1804 or ubuntu \u003e=16.04.4 LTS).\n2) python: 2.7 or 3.6. \n\n## Installation of packages:\n1) git clone git@github.com:XiaohanZhangCMU/axiom.git; cd axiom;   \n2) Add your (GPU/MPI)C++ project \"ABC\" to axiom/packages/ABC. Organize the codes into src and include.\n3) Write CMakeLists.txt in axiom/packages/ABC and write _axiom.cpp in a similar way as other packages to export the variables and methods to python.\n4) sh ./install_package \"your package name \" to compile. (You can also supply multiple package names and build them simultaneously. If no argument is given, all packages in axiom/packages will be built.)\n5) In python script, add sys.path.append('your_path_to/axiom/lib/') to the top.\n6) Enjoy!\n\n## Optional packages for visualization:\n1) pip install PyOpenGL PyOpenGL_accelerate (On Ubuntu or Linux need: sudo apt-get install python-opengl).\n2) python3 -m pip install Pillow   \n\n## Existing packages:\n1) zoo: A playground for simple pybind11 binding. \n2) tensor: GPU and boost::share_ptr for automatic gpu memeory allocation and syncronization. \n3) mdsw: MD++ (http://micro.stanford.edu/MDpp), a molecular dynamics simulator. Working with reinforcement learning. See  Python/frankMEP/SearchAlgorihtm.py.\n4) mdfem: Solve nonlinear neo-hookean FEM by minimizing potential energy.\n5) fem: A one dimensional elasticity FEM solver (to be generalized).  \n\n## Some Features:\n1) Implement greedy search algorithm for Frank Partial Dislocation energy barrier calculation in silicon thin film.\n2) mdsw interfaces with openAI/gym. On going: Deep Q network search algorithm for Frank Partial dislocation nucleation mechanism.\n3) tensor package enables automatic memory synchronization between GPU and CPU for tensors (same as Caffe).\n4) python/tests/View.py uses PyOpenG for visualization.\n5) Arrays can be exported as numpy arrays and modified in place (no deep memory copy is needed).\n\n\nBug reports or questions:\n\n1) Note: python script should not have the same name as the module because \"module load\" refers to the currently used python script, not the dynamic libraries.\n\nxiaohanzhang.cmu@gmail.com\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxiaohanzhangcmu%2Faxiom","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fxiaohanzhangcmu%2Faxiom","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxiaohanzhangcmu%2Faxiom/lists"}