{"id":44282419,"url":"https://github.com/venits/atometa","last_synced_at":"2026-02-10T22:01:20.353Z","repository":{"id":336920764,"uuid":"1151680786","full_name":"venits/atometa","owner":"venits","description":"3D Chemistry Simulation Engine - PhD Research Project for molecular visualization and dynamics","archived":false,"fork":false,"pushed_at":"2026-02-06T20:09:28.000Z","size":52,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-07T05:21:51.573Z","etag":null,"topics":["3d-visualization","chemistry","cmake","cpp","education","molecular-dynamics","opengl","phd-research","scientific-computing"],"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/venits.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":"SECURITY.md","support":null,"governance":null,"roadmap":"ROADMAP.md","authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-02-06T19:08:10.000Z","updated_at":"2026-02-06T19:12:54.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/venits/atometa","commit_stats":null,"previous_names":["bkhadr/atometa"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/venits/atometa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/venits%2Fatometa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/venits%2Fatometa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/venits%2Fatometa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/venits%2Fatometa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/venits","download_url":"https://codeload.github.com/venits/atometa/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/venits%2Fatometa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29319236,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T20:44:44.282Z","status":"ssl_error","status_checked_at":"2026-02-10T20:44:43.393Z","response_time":65,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["3d-visualization","chemistry","cmake","cpp","education","molecular-dynamics","opengl","phd-research","scientific-computing"],"created_at":"2026-02-10T22:01:09.869Z","updated_at":"2026-02-10T22:01:20.327Z","avatar_url":"https://github.com/venits.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Atometa\n\n3D Chemistry Simulation Engine for Research and Education\n\n---\n\n## Overview\n\nAtometa is an advanced molecular visualization and chemistry simulation engine developed as part of a PhD research project. Built with modern C++ and OpenGL, it provides real-time molecular dynamics simulation capabilities.\n\n## Project Vision\n\n- Academic Research: PhD thesis on molecular simulation and visualization\n- Education: Interactive chemistry teaching tool\n- Medical Applications: Drug discovery and molecular interaction analysis\n- Commercial Platform: Scalable solution for professional and educational use\n\n## Technology Stack\n\n- Language: C++17\n- Graphics API: OpenGL 3.3+\n- Build System: CMake 3.20+\n- Package Manager: vcpkg\n- Window/Input: GLFW 3.3+\n- UI Framework: ImGui (planned)\n- Math Libraries: GLM, Eigen\n\n## Required Libraries\n\n### Core Dependencies\n\n- GLFW 3.3+ - Window and input management\n- GLAD - OpenGL function loader\n- GLM 0.9.9+ - Mathematics (vectors, matrices, transformations)\n- ImGui 1.89+ - Immediate mode GUI framework\n- Eigen 3.4+ - Linear algebra for scientific computing\n- stb_image - Image loading utilities\n\n### Chemistry Libraries (Future)\n\n- Open Babel 3.1+ - Molecular file I/O (PDB, MOL, XYZ formats)\n- RDKit - Cheminformatics toolkit for drug discovery\n\n## Quick Start\n\n### Prerequisites\n\n1. Visual Studio 2019 or later with C++ Desktop Development\n2. CMake 3.20+\n3. vcpkg package manager\n4. Git\n\n### Installation Steps\n\n#### 1. Install vcpkg\n\n```cmd\ngit clone https://github.com/Microsoft/vcpkg.git C:\\vcpkg\ncd C:\\vcpkg\nbootstrap-vcpkg.bat\nvcpkg integrate install\n```\n\n#### 2. Install Dependencies\n\n```cmd\nvcpkg install glfw3:x64-windows\nvcpkg install glad:x64-windows\nvcpkg install glm:x64-windows\nvcpkg install imgui[glfw-binding,opengl3-binding]:x64-windows\nvcpkg install eigen3:x64-windows\nvcpkg install stb:x64-windows\n```\n\nInstallation time: 5-15 minutes\nDisk space required: Approximately 500 MB\n\n#### 3. Configure CMake\n\n```cmd\ncd C:\\atometa\ncmake -B build -S . -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake\n```\n\n#### 4. Build Project\n\n```cmd\ncmake --build build --config Release\n```\n\n#### 5. Open in Visual Studio\n\n```cmd\nstart build\\Atometa.sln\n```\n\nSet configuration to Release or Debug and press F5 to run.\n\n## Build Optimization\n\n### Method 1: Use Ninja Generator (Recommended)\n\nNinja is 30-50% faster than MSBuild.\n\n```cmd\nvcpkg install ninja:x64-windows\ncmake -G Ninja -B build -S . -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake\ncmake --build build\n```\n\n### Method 2: Enable ccache\n\nccache significantly speeds up rebuilds by caching compilation results.\n\n```cmd\nvcpkg install ccache:x64-windows\n```\n\nCMake will automatically detect and use ccache if available.\n\n### Method 3: Precompiled Headers\n\nPrecompiled headers are enabled by default in CMakeLists.txt. This reduces compilation time for frequently included headers like STL containers and GLM.\n\n### Method 4: Multi-processor Compilation\n\nAutomatically enabled for Visual Studio builds with the /MP flag. Uses all available CPU cores during compilation.\n\n## Project Structure\n\n```\nAtometa/\n├── src/                    Source code\n│   ├── core/              Core engine (Application, Window, Input, Logger)\n│   ├── renderer/          OpenGL rendering system\n│   ├── chemistry/         Chemistry simulation (Atom, Molecule, Bonds)\n│   └── ui/               ImGui user interface\n│\n├── include/Atometa/       Public headers\n│   ├── Core/\n│   ├── Renderer/\n│   ├── Chemistry/\n│   └── UI/\n│\n├── assets/                Resources\n│   ├── shaders/          GLSL shader files\n│   ├── models/           3D molecular models\n│   ├── textures/         Texture files\n│   └── branding/         Logo and branding assets\n│\n├── docs/                  Documentation\n│   ├── api/              API reference\n│   ├── research/         Research notes and papers\n│   └── tutorials/        User guides\n│\n├── research/              PhD research materials\n│   ├── papers/           Reference papers and literature\n│   ├── notes/            Research notes and observations\n│   └── experiments/      Experimental data and results\n│\n├── tests/                Unit tests\n│\n├── CMakeLists.txt        Build configuration\n├── vcpkg.json            Dependency manifest\n├── .gitignore            Git ignore rules\n└── LICENSE               MIT License\n```\n\n## Development Roadmap\n\n### Phase 1: Foundation (Months 1-3)\n- [x] Project setup and build system\n- [x] Core architecture (Application, Window, Input, Logger)\n- [ ] Basic OpenGL rendering pipeline\n- [ ] Camera system with orbital controls\n- [ ] ImGui integration\n\n### Phase 2: Chemistry Core (Months 3-6)\n- [ ] Atom and molecule data structures\n- [ ] Periodic table database\n- [ ] Bond visualization (single, double, triple bonds)\n- [ ] Molecular file I/O (XYZ, PDB formats)\n- [ ] Basic molecular editor\n\n### Phase 3: Simulation (Months 6-12)\n- [ ] Force field implementation (AMBER, UFF)\n- [ ] Molecular dynamics engine\n- [ ] Energy minimization algorithms\n- [ ] Collision detection and response\n\n### Phase 4: Advanced Features (Months 12-18)\n- [ ] Advanced rendering (surface, volumetric)\n- [ ] Quantum chemistry integration\n- [ ] Python scripting API\n- [ ] Performance optimization and GPU acceleration\n\n### Phase 5: Research and Publication (Months 18-24)\n- [ ] Thesis writing and documentation\n- [ ] Performance benchmarking\n- [ ] User studies and validation\n- [ ] Academic publications\n\n## Current Status\n\n| Component | Status | Progress |\n|-----------|--------|----------|\n| Build System | Complete | 100% |\n| Core Engine | In Progress | 25% |\n| Renderer | Planned | 0% |\n| Chemistry Core | Planned | 0% |\n| UI System | Planned | 0% |\n| Simulation | Planned | 0% |\n\n## Academic Context\n\nThis project is developed as part of a PhD program focusing on:\n\n- Computational chemistry and molecular dynamics\n- Real-time 3D visualization of chemical systems\n- Interactive educational tools for chemistry education\n- Scalable architecture for scientific computing\n\n### Research Applications\n\n1. Molecular Dynamics - Simulating atomic and molecular interactions\n2. Drug Discovery - Visualizing protein-ligand binding mechanisms\n3. Chemical Education - Interactive teaching and learning platform\n4. Materials Science - Studying molecular structures and properties\n\n## System Requirements\n\n### Minimum Requirements\n\n- Operating System: Windows 10/11 (64-bit)\n- CPU: Intel i5-4570 or equivalent (4 cores)\n- RAM: 8 GB\n- GPU: Intel HD Graphics 4600 or better (OpenGL 3.3+ support)\n- Disk Space: 2 GB free space\n\n### Recommended Requirements\n\n- CPU: Intel i7 or AMD Ryzen 7\n- RAM: 16 GB\n- GPU: Dedicated GPU with 2GB+ VRAM (NVIDIA GTX 1060 / AMD RX 580 or better)\n- Disk Space: 5 GB free space\n\n## Contributing\n\nWhile this is primarily a PhD research project, contributions are welcome.\n\n1. Fork the repository\n2. Create a feature branch\n3. Commit your changes\n4. Push to the branch\n5. Open a Pull Request\n\n## Issues \u0026 Feedback\n\nFound a bug or have an idea for a new feature?\n\n→ Open an issue here: [https://github.com/venits/atometa/issues/new](https://github.com/venits/atometa/issues/new)\n\nPlease use the provided templates:\n- Bug Report\n- Feature Request\n\nSearch existing issues first to avoid duplicates.\n\n## License\n\nThis project is licensed under the MIT License. See LICENSE file for details.\n\nThis allows commercial use, modification, distribution, and private use.\n\n## Author\n\nPhD Candidate\nDepartment of Chemistry\n\n## Acknowledgments\n\n- Academic supervisors and research committee\n- Open-source community (GLFW, ImGui, Dear ImGui, GLM, Eigen)\n- Chemistry and computational science communities\n- vcpkg maintainers\n\n---\n\nLast Updated: February 2026","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvenits%2Fatometa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvenits%2Fatometa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvenits%2Fatometa/lists"}