Package: amcess
Atomic and Molecular Cluster Energy Surface Sampler (AMCESS)Exploration of the Potential Energy Surface (PES) of molecules or atoms clusters is
a crucial step to analyze physical–chemistry properties and processes. The Atomic and
Molecular Energy Surface Sampler (AMCESS) is an end-to-end package implemented
in Python 3.9 to generate candidate structures for the critical points sampling of the
PES. The amcess main purpose is to be a
user friendly package, easy to install, import, and run, available in most platforms and
open-source. As a Python module, amcess can be integrated into any workflow. This
package has code reviews with unit testing and continuous integration, code coverage
tools, and automatically keeps documentation up–to–date.Molecular cluster of ibuprofen and six water molecules
  [doi: 10.1063/1.4874258]DescriptionThe amcess package uses simple input files and automates common procedures to
explore the PES using the Simulated Annealing, Simplicial Homology Global Optimiza-
tion (SHGO), and Bayesian Optimization to generate candidate structures for any kind
of critical point, such as local minima or transition states. The package also allows the
user to perform local searches around defined regions. The PES is generated computing
the electronic energy using standard and powerful quantum chemistry packages such as
PySCF and Psi4, also implemented in Python.Technical DocumentationTechnical documents behind this project can be accessedhere.RequirementsFirst you should install the required python packages- attrs==21.2
  - scipy==1.7.1
  - numpy==1.21.2
  - pyscf==1.7.6.post1
  - h5py==3.1.0
  - pyberny==0.6.3
  - geomeTRIC==0.9.7.2
  - GPyOpt==1.2.6
  - pyDOE==0.3.8
  - matplotlib==3.4.2check the filerequirements.txt. For developer, you should installrequirements_dev.txt.InstallationAMCESS isPython 3.9packageInstall virtual environment:python -m venv venvActivate virtual environment:source venv/bin/activateInstall the packages:pip install amcessRun AMCESS (check some examples below)For developer only, install dependencies:pip install -r requirements.txt -r requirements_dev.txtRun all test:tox==3.24.3UsageA detail workflow is provide intoworkflowdirectory. It has a list of Jupyter notebook with detail examples about AMCESS tools and capabilities.Workflow:Getting starting with atoms and molecules properties.Notebook (binder):01_importing_atoms_and_molecules.ipynbTranslating and rotating atoms and molecules.Notebook (binder):02_move_rotate_molecules.ipynbMoving Molecules randomly from a Cluster.Notebook (binder):03_move_rotate_cluster.ipynbFreezing any molecule and redefine its sphere center.Notebook (binder):04_freeze_molecule_redefine_center.ipynbInitialize a cluster avoiding atomic overlappingNotebook (binder):05_initialize_cluster_and_move_molecule.ipynbRoadmapSome of the ideas to keep growing are:Integration withRDKit(multiple format input)Results: geometrical analysis (clustering, k-nearest, k-means, etc.)ContributingThe easiest way to get help with the project is to join the #amcess
channel on Discord.We hang out there and you can get real-time help with your projects.
The other good way is to open an issue on GitLab.Discord:https://discord.gg/vxQQCjpgGitLab:https://gitlab.com/ADanianZE/amcess/issuesLicenceGNU General Public License v3 (GLPv3)Authors and AcknowledgmentMain authors: Alejandra Mendez, Juan Jose Aucar, Daniel Bajac, César Ibargüen, Andy Zapata, Edison Florez (edisonffh@mail.com)Project StatusUnder developmentASCEC (FORTRAN 77 version)A previous version of AMCESS, called ASCEC[1](spanish acronym
Annealing Simulado con Energía Cuántica) was written in FORTRAN77 and
was successfully used in the wide range of research and academic applications.
From atomic cluster to molecular cluster, the ASCEC package has produced
novel results (structure never seen before) published in the literature. Read more onASCEC publications.You could check the directoryASCECV3ASCECV3/
|---papers/  
|---p_ascec/
|---examples/
      |---adf     
      |---dalton  
      |---g03
      |---gamess
      |---nwchemReferences[1]J Pérez and A Restrepo. Ascec v–02: annealing simulado con energía cuántica. Property, development and implementation: Grupo de Química–Física Teórica, Instituto de Química, Universidad de Antioquia: Medellín, Colombia, 2008.