amcess 0.1.1

Description:

amcess 0.1.1

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]



Description
The 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 Documentation
Technical documents behind this project can be accessed here.
Requirements
First 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==3.4.2

check the file requirements.txt. For developer, you should install requirements_dev.txt.
Installation
AMCESS is Python 3.9 package


Install virtual environment:
python -m venv venv


Activate virtual environment:
source venv/bin/activate


Install the packages:
pip install amcess


Run AMCESS (check some examples below)


For developer only, install dependencies:
pip install -r requirements.txt -r requirements_dev.txt


Run all test:
tox==3.24.3


Usage
A detail workflow is provide into workflow directory. 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.ipynb


Translating and rotating atoms and molecules.

Notebook (binder): 02_move_rotate_molecules.ipynb


Moving Molecules randomly from a Cluster.

Notebook (binder): 03_move_rotate_cluster.ipynb


Freezing any molecule and redefine its sphere center.

Notebook (binder): 04_freeze_molecule_redefine_center.ipynb


Initialize a cluster avoiding atomic overlapping

Notebook (binder): 05_initialize_cluster_and_move_molecule.ipynb



Roadmap
Some of the ideas to keep growing are:

Integration with RDKit (multiple format input)
Results: geometrical analysis (clustering, k-nearest, k-means, etc.)

Contributing
The 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/vxQQCjpg


GitLab: https://gitlab.com/ADanianZE/amcess/issues


Licence
GNU General Public License v3 (GLPv3)
Authors and Acknowledgment
Main authors: Alejandra Mendez, Juan Jose Aucar, Daniel Bajac, César Ibargüen, Andy Zapata, Edison Florez ([email protected])
Project Status
Under development

ASCEC (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 on ASCEC publications.
You could check the directory ASCECV3
ASCECV3/
|---papers/
|---p_ascec/
|---examples/
|---adf
|---dalton
|---g03
|---gamess
|---nwchem

References

[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.