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    "info": {
        "author": " Edison Florez, Andy Zapata, Daniel Bajac, Alejandra Mendez, Cesar Ibarguen, Jos\u00e9 Aucar ",
        "author_email": " edisonffhc@gmail.com, danianescobarv@gmail.com",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: Implementation :: CPython",
            "Topic :: Scientific/Engineering"
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        "description": "<!-- [![Python 3.9](https://img.shields.io/badge/python-3.9-blue.svg)](https://www.python.org/downloads/release/python-390/)\n![Gitlab pipeline status](https://img.shields.io/gitlab/pipeline/ADanianZE/ascec/main?style=plastic)\n[![pipeline status](https://gitlab.com/ADanianZE/ascec/badges/main/pipeline.svg)](https://gitlab.com/ADanianZE/ascec/-/commits/main)\n![Gitlab code coverage](https://img.shields.io/gitlab/coverage/ADanianZE/ascec/main?style=plastic)\n[![Coverage Status](https://coveralls.io/repos/gitlab/ADanianZE/ascec/badge.svg?branch=main)](https://coveralls.io/gitlab/ADanianZE/ascec?branch=main)\n[![coverage report](https://gitlab.com/ADanianZE/ascec/badges/main/coverage.svg)](https://gitlab.com/ADanianZE/ascec/-/commits/main)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F01_importing_atoms_and_molecules.ipynb)\n![GitLab tag (latest by date)](https://img.shields.io/gitlab/v/tag/ADanianZE/ascec?style=plastic)\n[![mypy: checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n![Pod License](https://img.shields.io/badge/license-MIT-blue.svg)  -->\n\n<!-- ![Atomic and Molecular Cluster Energy Surface Sampler](./docs/_static/amcess_logo.png) -->\n\n\n<div align=\"center\">\n  <a href=http://mypy-lang.org/>\n  <img src=\"http://www.mypy-lang.org/static/mypy_badge.svg\"></a>\n  <a href=https://github.com/psf/black>\n  <img src=\"https://img.shields.io/badge/code%20style-black-000000.svg\"></a>\n  <br>\n  <a href=https://www.python.org/downloads/release/python-390/>\n  <img src=https://img.shields.io/badge/python-3.9-blue.svg></a>\n  <a href=https://www.gnu.org/licenses/gpl-3.0>\n  <img src=\"https://img.shields.io/badge/License-GPLv3-blue.svg\"></a>\n  <a href=https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F01_importing_atoms_and_molecules.ipynb>\n  <img src=\"https://mybinder.org/badge_logo.svg\"></a>\n  <br>  \n  <a href=https://img.shields.io/gitlab/pipeline/ADanianZE/ascec/main?style=plastic>\n  <img src=\"https://img.shields.io/gitlab/pipeline/ADanianZE/ascec/main?style=plastic\"></a>\n  <a href=https://gitlab.com/ADanianZE/ascec/-/commits/main>\n  <img src=\"https://gitlab.com/ADanianZE/ascec/badges/main/pipeline.svg\"></a>\n  <a href=https://img.shields.io/gitlab/coverage/ADanianZE/ascec/main?style=plastic>\n  <img src=\"https://img.shields.io/gitlab/coverage/ADanianZE/ascec/main?style=plastic\"></a>\n  <a href=https://coveralls.io/gitlab/ADanianZE/ascec?branch=main>\n  <img src=\"https://coveralls.io/repos/gitlab/ADanianZE/ascec/badge.svg?branch=main\"></a>\n</div>\n\n---\n\n<div align=\"center\">\n  <a href=\"Atomic and Molecular Cluster Energy Surface Sampler\">\n  <img width=\"400\" height=\"200\" src=\"https://gitlab.com/ADanianZE/amcess/-/raw/main/docs/source/_static/amcess_logo.png\"></a>\n  <br>\n</div>\n\n---\n\n<div align=\"center\">\n  <h1> Atomic and Molecular Cluster Energy Surface Sampler (AMCESS) </h1>\n</div>\n\nExploration of the Potential Energy Surface (PES) of molecules or atoms clusters is\na crucial step to analyze physical\u2013chemistry properties and processes. The Atomic and\nMolecular Energy Surface Sampler (AMCESS) is an end-to-end package implemented\nin Python 3.9 to generate candidate structures for the critical points sampling of the\nPES. The amcess main purpose is to be a\nuser friendly package, easy to install, import, and run, available in most platforms and\nopen-source. As a Python module, amcess can be integrated into any workflow. This\npackage has code reviews with unit testing and continuous integration, code coverage\ntools, and automatically keeps documentation up\u2013to\u2013date. \n\n\n<div align=\"center\">\n  <img width=\"200\" height=\"80\" src=\"https://gitlab.com/ADanianZE/amcess/-/raw/main/docs/source/_static/ibuprofen.png\" VSPACE=50 HSPACE=10>\n  <img width=\"350\" height=\"200\" src=\"https://gitlab.com/ADanianZE/amcess/-/raw/main/docs/source/_static/ibu_w6_white.gif\" HSPACE=20>\n  <br>\n  Molecular cluster of ibuprofen and six water molecules\n  [<a href=\"http://www.doi.org/10.1063/1.4874258\">doi: 10.1063/1.4874258</a>]\n  <br>\n  <br>\n</div>\n\n### Description\n\nThe amcess package uses simple input files and automates common procedures to\nexplore the PES using the Simulated Annealing, Simplicial Homology Global Optimiza-\ntion (SHGO), and Bayesian Optimization to generate candidate structures for any kind\nof critical point, such as local minima or transition states. The package also allows the\nuser to perform local searches around defined regions. The PES is generated computing\nthe electronic energy using standard and powerful quantum chemistry packages such as\nPySCF and Psi4, also implemented in Python.\n\n### Technical Documentation\nTechnical documents behind this project can be accessed [here](https://adanianze.gitlab.io/amcess).\n\n\n### Requirements\n\nFirst you should install the required python packages \n\n      - attrs==21.2\n      - scipy==1.7.1\n      - numpy==1.21.2\n      - pyscf==1.7.6.post1\n      - h5py==3.1.0\n      - pyberny==0.6.3\n      - geomeTRIC==0.9.7.2\n      - GPyOpt==1.2.6\n      - pyDOE==0.3.8\n      - matplotlib==3.4.2\n\ncheck the file `requirements.txt`. For developer, you should install `requirements_dev.txt`.\n\n### Installation\nAMCESS is **Python 3.9** package\n\n1. Install virtual environment:\n\n    ```python -m venv venv```\n\n2. Activate virtual environment:\n\n    ```source venv/bin/activate```\n\n3. Install the packages:\n\n      ```pip install amcess```\n\n4. Run AMCESS (check some examples below)\n\n5. For developer only, install dependencies:\n\n      ```pip install -r requirements.txt -r requirements_dev.txt```\n\n6. Run all test:\n\n      ``tox==3.24.3``\n\n### Usage\n\nA detail workflow is provide into `workflow` directory. It has a list of Jupyter notebook with detail examples about AMCESS tools and capabilities.\n\nWorkflow:\n1. Getting starting with atoms and molecules properties. \n      - Notebook ([binder](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F01_importing_atoms_and_molecules.ipynb)): `01_importing_atoms_and_molecules.ipynb` \n2. Translating and rotating atoms and molecules. \n      - Notebook ([binder](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F02_move_rotate_molecules.ipynb)): `02_move_rotate_molecules.ipynb` \n3. Moving Molecules randomly from a Cluster. \n      - Notebook ([binder](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F03_move_rotate_cluster.ipynb)): `03_move_rotate_cluster.ipynb` \n4. Freezing any molecule and redefine its sphere center. \n      - Notebook ([binder](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F04_freeze_molecule_redefine_center.ipynb)): `04_freeze_molecule_redefine_center.ipynb` \n5. Initialize a cluster avoiding atomic overlapping\n      - Notebook ([binder](https://mybinder.org/v2/gl/ADanianZE%2Fascec/main?filepath=workflow%2F05_initialize_cluster_and_move_molecule.ipynb)): `05_initialize_cluster_and_move_molecule.ipynb` \n\n## Roadmap\nSome of the ideas to keep growing are:\n\n* Integration with **RDKit** (multiple format input)\n* Results: geometrical analysis (clustering, k-nearest, k-means, etc.)\n\n## Contributing\nThe easiest way to get help with the project is to join the #amcess\nchannel on Discord.\n\nWe hang out there and you can get real-time help with your projects.\nThe other good way is to open an issue on GitLab.\n\n- Discord: https://discord.gg/vxQQCjpg\n\n- GitLab:  https://gitlab.com/ADanianZE/amcess/issues\n\n### Licence\nGNU General Public License v3 (GLPv3)\n\n### Authors and Acknowledgment\nMain authors: Alejandra Mendez, Juan Jose Aucar, Daniel Bajac, C\u00e9sar Ibarg\u00fcen, Andy Zapata, Edison Florez (_edisonffh@mail.com_)\n\n### Project Status\n\nUnder development\n\n\n\n\n---\n\n## ASCEC (FORTRAN 77 version)\n\nA previous version of AMCESS, called ASCEC [[1]](#1) (spanish acronym \nAnnealing Simulado con Energ\u00eda Cu\u00e1ntica) was written in FORTRAN77 and \nwas successfully used in the wide range of research and academic applications. \nFrom atomic cluster to molecular cluster, the ASCEC package has produced \nnovel results (structure never seen before) published in the literature. Read more on [ASCEC publications](https://scholar.google.com/scholar?start=0&q=%22ascec%22,+annealing&hl=en&as_sdt=0,5).\n\n\nYou could check the directory [ASCECV3](https://gitlab.com/ADanianZE/ascec/-/tree/main/ASCECV3)\n\n```\nASCECV3/\n|---papers/  \n|---p_ascec/\n|---examples/\n      |---adf     \n      |---dalton  \n      |---g03\n      |---gamess\n      |---nwchem\n```\n### References\n<div style=font-size:12px>\n      <a id=\"1\">[1]</a> \n      J P\u00e9rez and A Restrepo. Ascec v\u201302: annealing simulado con energ\u00eda cu\u00e1ntica. Property, development and implementation: Grupo de Qu\u00edmica\u2013F\u00edsica Te\u00f3rica, Instituto de Qu\u00edmica, Universidad de Antioquia: Medell\u00edn, Colombia, 2008.\n<br>\n</div>\n\n",
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