Cun-PES repository
João Paulo A. de Mendonça, USP
Tuanan C. Lourenço, USP
Felipe V. Calderan, UNIFESP
Marcos G. Quiles, UNIFESP
Juarez L. F. Da Silva, USP
Nanoclusters are remarkably promising for the capture and activation of small molecules for fuel production or for the use as a precursor for other chemicals of high commercial value. Since this process occurs under a wide variety of experimental conditions, full comprehension of the stability and phase transitions that these systems can undergo is detrimental to the development of successful technological applications. In this work, we proposed a theoretical framework to explore the potential energy surface and configuration space of nanoclusters to map the most important morphologies presented by those systems and the phase transitions between them. To do so, a fully automated process was developed that combined global optimization techniques, classical molecular dynamics, and unsupervised machine learning. To showcase these capabilities of the approach, we explored the example of copper nanoclusters Cu_n where n = 13, 38, 55, 75, 98, 102, 147. We not only reported a graphical potential energy surface for each size, but also explored the topology of the configurations space via structural and thermodynamic analysis. The effect of size on the PES and the critical temperature for solid-liquid phase transitions was also reported, highlighting the impact of magic numbers on those quantities.
Use K-Means with energy and silhouette criteria to cluster all local minima visited in BHMC process (obtained from GOTNANO global optimization runs).
Apply t-SNE on MD data to plot a 2D projection of the data, potential energy surface and 2D density of samples estimation. 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.
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.
Small set of tools to work with XYZ files.
Bash Script that executes all the necessary files.
To install the necessary dependencies, execute:
pip3 install -r requirements.txt
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