Cun-PES

Code sharing repository associated with the manuscript Theoretical Framework based on Molecular Dynamics and Data Mining Analyses to the Study of the Potential Energy Surfaces of Finite-size Particles (under submission and peer-reviewing process).

Authors

João Paulo A. de Mendonça^a, Tuanan C. Lourenço^a, Felipe V. Calderan^b, Marcos G. Quiles^b, Juarez L. F. Da Silva^a

^a São Carlos Institute of Chemistry, University of São Paulo, P.O. Box 780, 13560-970, São Carlos, SP, Brazil

^b Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil

Project Files

00_lmkmeans.py

In the original context: Use k-means with energy and silhouette criteria to cluster all local minima visited in BHMC process (obtained from GOTNANO in-house global optimization code).

I/O information: Requires a structured input composed of a folder of XYZ files and a 2-columns ASCII file with file names (column 0) and respective Potential Energies (column 1).

01_tsne.py

In the original context: Apply t-SNE on MD data to plot a 2D projection of the data, potential energy surface and 2D density of samples estimation.

I/O information: Also requires the transformation of MD data in a structured repository of structures and energies, following the same format as the one for 00_lmkmeans.py. This script also outputs XYZ coordinates, where X and Y are 2D coordinates of the t-SNE projection of the MD data and Z is the energy data.

02_treat_tsne.py

In the original context: Cluster t-SNE data with DBSCAN and remove the noise using kNN. This produces an output containing the ID and label of each element, post-kNN and a treated t-SNE plot.

I/O information: This code is supposed to be run after 01_tsne.py, using its inputs and outputs.

libs/xyz_files.py

Small set of tools to work with XYZ files to be imported in the other Python codes.

run.sh

Bash Script that executes all the necessary files. It runs over the consolidated input exemplified in example_settings.ini.

Install dependencies

To install the necessary dependencies, execute:

pip3 install -r requirements.txt

Run the program

When running the program for the first time, make sure that run.sh is executable with:

chmod +x run.sh

After configuring the program inside a settings.ini (see example_settings.ini) file, run:

./run.sh everything settings.ini